OK doods.... this is my HYPOTHESIS... but it worked for me.... just like hukd on fonix
If you have a "custom.cfg" file in yer /main directory OR ANY OTHER config file you might exec from a shortcut (server.cfg's exempt) then I suggest this:
Open BOTH unnamedsoldier.cfg (main/configs) AND whatever/custom.cfg (/main) in a text editor. (yes that's two INSTANCES... or different windows)
Compare the two text files and make sure there are no DUPLICATE lines/settings....having established that cut/paste EVERYTHING you want to keep from "custom.cfg" into /mohaa/main/configs/unnamedsoldier.cfg file. SAVE the file and try it again. (delete custom.cfg... you already transfered the info in it)
This (judging from console output) is what is happening to you.....
ALL q3 based games look for an "custom.cfg" by DEFAULT (as far as i know)
When your game starts it reads unnmaedsoldier/cfg FIRST then AFTERWARDS it reads your "custom.cfg"
When you change settings (resolution for example) the changes are WRITTEN to "unnamedsoldier.cfg (the 1st to be read)... so as the game loads is reads your CHANGES then it reads 'custom.cfg' which is PROBABLY resetting those changes to whatever is specified in "custom".cfg
(ie: your OLD settings)
I hope this makes sense.... I suck at explanations....
GI Jerk