Addons not loading automatically depending upon content?

[makermod1]

So, recently some of my addons refuse to actually initialize unless I trigger the autorefresh feature on the server by editing a file and changing it back. What would be causing this? This includes entities which cannot be used until an auto refresh is triggered, or weapon stats which don't show until triggered. (They also randomly start working hours later)
I know this is vague, but I can't narrow it down to anything. To be honest I don't remember when it started happening, and any in house addons worked fine prior to this.. :|

I've done no major changes to my gamemode base either.

The only non custom addons I've added to the server have been the following:
Customizable Weaponry 2.0
ErrorCleanse (Why?)
Stunner SWEP (Maybe)
Fireworks
Box vis
VJ Base (Huge addon, lua wise. Maybe?)
No More Room In Hell SNPCs
Zombie SNPCs
Military SNPCs - United States
Military SNPCs - Insurgents
WAC Aircraft + Community pack 4 and 3(Maybe?)

[Acecool]

Your load order is incorrect, or Lua file limit is reached, or functions are being overwritten, or file-names are being re-used / overwritten..

Here's a basic example of things only working after auto-refresh ( load-order example ):
[url]https://dl.dropboxusercontent.com/u/26074909/tutoring/includes/file_only_works_on_autorefresh_possible_reasons.lua.html[/url]

Give us a condebug, there may be errors or other clues as to what is causing this.