Compiler skipping bones?

[kirono]

I followed Mario's guide to ragdoll, and I did everything correctly, but when I try compiling my model, the compiler completely ignore the "Head", "Neck", "ShoulderR", and "ShoulderL" bones? Are their any ideas of what might my causing the problem?
Here is what I mean:

Processing jointed collision model
Waist                    (311 verts, 10 convex elements) volume: 4062.20
Breast                   (3066 verts, 10 convex elements) volume: 8151.58
WARNING: Model has 2-dimensional geometry (less than 0.500 inches thick on any axis)!!!
WARNING: Model has 2-dimensional geometry (less than 0.500 inches thick on any axis)!!!
WARNING: Error with convex elements of c:\program files (x86)\steam\steamapps\kironohasama\half-life 2\hl2\models\Aeon/phymodel.smd, building single convex!!!!
UpperArmR                (232 verts, 10 convex elements) volume: 708.46
LowerArmR                (340 verts, 10 convex elements) volume: 764.84
HandR                    (1188 verts, 10 convex elements) volume: 329.74
UpperArmL                (224 verts, 10 convex elements) volume: 639.43
LowerArmL                (367 verts, 10 convex elements) volume: 794.85
HandL                    (1188 verts, 10 convex elements) volume: 328.93
ThighR                   (147 verts, 6 convex elements) volume: 1749.35
ShinR                    (468 verts, 6 convex elements) volume: 2276.99
FootR                    (116 verts, 1 convex elements) volume: 169.89
ThighL                   (144 verts, 6 convex elements) volume: 1689.66
ShinL                    (468 verts, 6 convex elements) volume: 2283.39
FootL                    (116 verts, 1 convex elements) volume: 169.90
Collision model completed.

[IMG]http://img.photobucket.com/albums/v643/Caboose117/compileproblem.png[/IMG]

[Artfunkel]

Studiomdl will optimise out any bones that don't have attached vertices. Make sure that isn't happening.

[kirono]

[QUOTE=Varsity;34989778]Studiomdl will optimise out any bones that don't have attached vertices. Make sure that isn't happening.[/QUOTE]
Ok, I tried assigning some vertices to the Shoulders and Neck and it recognized those bones, but it still ignored the "Head" bone, even though it has vertices assigned to it.

[Deunan]

Try jointmerging the neck and head bones to see what it does. (so you know that it's due to the neck or not)

[kirono]

[QUOTE=wraithcat;34997735]Try jointmerging the neck and head bones to see what it does. (so you know that it's due to the neck or not)[/QUOTE]

K so I tried that command, and it worked for the most part, but it caused the head to act as part the neck, so posing looked a little weird. I checked the .max files to see if any of the bones had the same name, but they were fine. I also checked the rigging of vertices and they seemed fine too.

[Deunan]

Well if jointmerging the two fixes the issue then something is wrong with either the neck or head bone. My money is on the neck one.

[kirono]

So then should I try deleting the two bones and re create them and assign vertices?

[kirono]

Sorry for the Double post, but I tried deleting the bones, creating new ones with different names, reassigned vertices, and the compiler STILL skipped the head bone.

Edit: I found the problem. I tried using wunderboy's SMD exporter instead of cannonfodder's. wunderboy's kept messing up the bones. It turned out perfect this time. Thanks for everyone's suggestion and efforts. Moderators can lock this thread.