3D Skybox causing some light issues

Modifying an old tnb map for another community, run into some strange light issues, but before I delve into them, I must say that I’m 95% certain the VMF isn’t from a decompiled version of the original (it still has its’ custom visgroups, which, IIRC, don’t come with decompiled VMF’s), and that from the source I got the files from (was a thread here somewhere), it was mentioned that you could do whatever with them.

That aside, whenever a 3D skybox is present, somewhere, somehow, the lighting gets fucked in certain places to varying degrees, however it’s almost always sunlight doing this.
Examples:

http://cloud.steampowered.com/ugc/614967448829272106/5B360B7664A0E68FED859B4B17A54AC60AA48445/
http://cloud.steampowered.com/ugc/614967448829273608/607D8B25C31ACDBA5EF39251283EC5984321B713/

Here’s what it’s supposed to look like:

http://cloud.steampowered.com/ugc/614967448829387511/07F6955C237ADBC1E0B2F18DF9EE03E79912C0BB/
http://cloud.steampowered.com/ugc/614967448829389058/F181767027A5AD39A5EF174A6675EDAC2D30A522/

Now, listing things I’ve done:

Alt + P just reports misc. keyvalue errors, namely gmod_allowphysgun
Interlopers reports a Zero Area Child Patch but no location of it.
Deleting the 3D skybox sets the lighting correctly (see second set of images)
Compile options on VRAD: -LargeDispSampleRadius -softsun 2 -textureshadows -StaticPropPolys -noskyboxrecurseReplacing the skybox from version 1 of the original tnb map to version 2’s skybox worked for a bit, but now back to square one
Ensured there was no light_environment in the skybox (there’s one in the actual world area)

Compile log:





================== VBSP ==================






materialPath: c:\program files (x86)\steam\steamapps\mike086\half-life 2 episode two\ep2\materials
Loading C:\Users\KFrohman\Documents\rp_city45_catalyst_x1c.vmf
ConVarRef mat_reduceparticles doesn't point to an existing ConVar
Could not locate 'GameData' key in c:\program files (x86)\steam\steamapps\mike086\half-life 2 episode two\ep2\gameinfo.txt
Patching WVT material: maps/rp_city45_catalyst_x1c/nature/blenddirtgrass001a_wvt_patch
Patching WVT material: maps/rp_city45_catalyst_x1c/nature/canal_reeds_wvt_patch
Patching WVT material: maps/rp_city45_catalyst_x1c/nature/blendgrassdirt01_wvt_patch
Patching WVT material: maps/rp_city45_catalyst_x1c/dev/dev_blendmeasure_wvt_patch
fixing up env_cubemap materials on brush sides...
0...1...2...3...4...5...6...7...8...9...100...1...2...3...4...5...6...7...8...9...10Processing areas...done (0)
Building Faces...done (0)
Chop Details...done (0)
Find Visible Detail Sides...
Merged 1086 detail faces...done (0)
Merging details...done (0)
FixTjuncs...
PruneNodes...
WriteBSP...
done (2)
writing C:\Users\KFrohman\Documents\rp_city45_catalyst_x1c.prt...Building visibility clusters...
done (0)
Creating default LDR cubemaps for env_cubemap using skybox materials:
   skybox/sky_day01_04_hdr*.vmt
 ! Run buildcubemaps in the engine to get the correct cube maps.
Creating default HDR cubemaps for env_cubemap using skybox materials:
   skybox/sky_day01_04_hdr*.vmt
 ! Run buildcubemaps in the engine to get the correct cube maps.
Finding displacement neighbors...
Finding lightmap sample positions...
Displacement Alpha : 0...1...2...3...4...5...6...7...8...9...10
Building Physics collision data...
done (2) (2248512 bytes)
Error! prop_static using model "models/props_c17/furniturecouch001a.mdl", which must be used on a dynamic entity (i.e. prop_physics). Deleted.
Error loading studio model "models/props_c17/furniturecouch001a.mdl"!
Error! prop_static using model "models/props_rooftop/sign_letter_h001.mdl", which must be used on a dynamic entity (i.e. prop_physics). Deleted.
Error loading studio model "models/props_rooftop/sign_letter_h001.mdl"!
Placing detail props : 0...1...2...3...4...5...6...7...8...9Material NATURE/CANAL_REEDS uses unknown detail object type canal_reeds!
Material NATURE/CANAL_REEDS uses unknown detail object type canal_reeds!
Material NATURE/CANAL_REEDS uses unknown detail object type canal_reeds!
Material NATURE/CANAL_REEDS uses unknown detail object type canal_reeds!
...10
Compacting texture/material tables...
Reduced 15616 texinfos to 7088
Reduced 1830 texdatas to 1283 (105589 bytes to 73846)
Writing C:\Users\KFrohman\Documents\rp_city45_catalyst_x1c.bsp
18 seconds elapsed


================== VVIS ==================








8 threads
reading c:\users\kfrohman\documents\rp_city45_catalyst_x1c.bsp
reading c:\users\kfrohman\documents\rp_city45_catalyst_x1c.prt
2658 portalclusters
6368 numportals
0...1...2...3...4...5...6...7...8...9...100...1...2...3...4...5...6...7...8...9...10Optimized: 3382 visible clusters (0.00%)
Total clusters visible: 504117
Average clusters visible: 189
Building PAS...
Average clusters audible: 741
visdatasize:642795  compressed from 1786176
writing c:\users\kfrohman\documents\rp_city45_catalyst_x1c.bsp
5 minutes, 11 seconds elapsed


================== VRAD ==================








[Reading texlights from 'lights.rad']
[48 texlights parsed from 'lights.rad']


Loading c:\users\kfrohman\documents\rp_city45_catalyst_x1c.bsp
24992 faces
1 degenerate faces
2590395 square feet [373016960.00 square inches]
9 Displacements
16068 Square Feet [2313824.25 Square Inches]
24991 patches before subdivision
zero area child patch
zero area child patch
275241 patches after subdivision
1309 direct lights
0...1...2...3...4...5...6...7...8...9...100...1...2...3...4...5...6...7...8...9...10transfers 30633938, max 1411
transfer lists: 233.7 megs
0...1...2...3...4...5...6...7...8...9...10    Bounce #1 added RGB(795667, 670166, 391042)
0...1...2...3...4...5...6...7...8...9...10    Bounce #2 added RGB(131792, 98147, 46843)
0...1...2...3...4...5...6...7...8...9...10    Bounce #3 added RGB(30526, 20922, 8237)
0...1...2...3...4...5...6...7...8...9...10    Bounce #4 added RGB(8518, 5465, 1811)
0...1...2...3...4...5...6...7...8...9...10    Bounce #5 added RGB(2754, 1659, 470)
0...1...2...3...4...5...6...7...8...9...10    Bounce #6 added RGB(968, 547, 134)
0...1...2...3...4...5...6...7...8...9...10    Bounce #7 added RGB(361, 191, 41)
0...1...2...3...4...5...6...7...8...9...10    Bounce #8 added RGB(140, 69, 13)
0...1...2...3...4...5...6...7...8...9...10    Bounce #9 added RGB(56, 26, 5)
0...1...2...3...4...5...6...7...8...9...10    Bounce #10 added RGB(23, 10, 2)
0...1...2...3...4...5...6...7...8...9...10    Bounce #11 added RGB(10, 4, 1)
0...1...2...3...4...5...6...7...8...9...10    Bounce #12 added RGB(4, 2, 0)
0...1...2...3...4...5...6...7...8...9...10    Bounce #13 added RGB(2, 1, 0)
0...1...2...3...4...5...6...7...8...9...10    Bounce #14 added RGB(1, 0, 0)
Build Patch/Sample Hash Table(s).....Done<0.0849 sec>
0...1...2...3...4...5...6...7...8...9...10FinalLightFace Done
744 of 756 (98% of) surface lights went in leaf ambient cubes.
0...1...2...3...4...5...6...7...8...9...10Writing leaf ambient...done
Ready to Finish


Object names       Objects/Maxobjs  Memory / Maxmem  Fullness 
------------       ---------------  ---------------  -------- 
models                 302/1024        14496/49152    (29.5%) 
brushes               6118/8192        73416/98304    (74.7%) 
brushsides           43429/65536      347432/524288   (66.3%) 
planes               24392/65536      487840/1310720  (37.2%) 
vertexes             41454/65536      497448/786432   (63.3%) 
nodes                 9997/65536      319904/2097152  (15.3%) 
texinfos              7088/12288      510336/884736   (57.7%) 
texdata               1283/2048        41056/65536    (62.6%) 
dispinfos                9/0            1584/0        ( 0.0%) 
disp_verts             865/0           17300/0        ( 0.0%) 
disp_tris             1440/0            2880/0        ( 0.0%) 
disp_lmsamples       39814/0           39814/0        ( 0.0%) 
faces                24992/65536     1399552/3670016  (38.1%) 
hdr faces                0/65536           0/3670016  ( 0.0%) 
origfaces            17621/65536      986776/3670016  (26.9%) 
leaves               10300/65536      329600/2097152  (15.7%) 
leaffaces            30712/65536       61424/131072   (46.9%) 
leafbrushes          13904/65536       27808/131072   (21.2%) 
areas                   32/256           256/2048     (12.5%) 
surfedges           191718/512000     766872/2048000  (37.4%) 
edges               117583/256000     470332/1024000  (45.9%) 
LDR worldlights       1309/8192       115192/720896   (16.0%) 
HDR worldlights          0/8192            0/720896   ( 0.0%) 
leafwaterdata            0/32768           0/393216   ( 0.0%) 
waterstrips           2175/32768       21750/327680   ( 6.6%) 
waterverts               0/65536           0/786432   ( 0.0%) 
waterindices         41130/65536       82260/131072   (62.8%) 
cubemapsamples         129/1024         2064/16384    (12.6%) 
overlays                85/512         29920/180224   (16.6%) 
LDR lightdata         [variable]    15002272/0        ( 0.0%) 
HDR lightdata         [variable]           0/0        ( 0.0%) 
visdata               [variable]      642795/16777216 ( 3.8%) 
entdata               [variable]      608708/393216   (154.8%) VERY FULL!
LDR ambient table    10300/65536       41200/262144   (15.7%) 
HDR ambient table    10300/65536       41200/262144   (15.7%) 
LDR leaf ambient     34548/65536      967344/1835008  (52.7%) 
HDR leaf ambient     10300/65536      288400/1835008  (15.7%) 
occluders                0/0               0/0        ( 0.0%) 
occluder polygons        0/0               0/0        ( 0.0%) 
occluder vert ind        0/0               0/0        ( 0.0%) 
detail props          [variable]           1/12       ( 8.3%) 
static props          [variable]           1/93260    ( 0.0%) 
pakfile               [variable]    14268348/0        ( 0.0%) 
physics               [variable]     2248512/4194304  (53.6%) 
physics terrain       [variable]        2463/1048576  ( 0.2%) 


Level flags = 0


Total triangle count: 70774
Writing c:\users\kfrohman\documents\rp_city45_catalyst_x1c.bsp
3 minutes, 15 seconds elapsed




I hope I can get this sorted because it’s starting to do my head in, mapper OCD and whatnot.
Feel free to ask questions if you need info. Hopefully I stuck this in the right place.

Should probably mention that the gammy lighting areas are only surface lit - that is, I could walk in there and my viewmodel won’t adjust for the change in light, and I could place models in there that would simply act as if they are in shadow (like they’re supposed to be).