does your resolution reset everytime you load the game? i just spent the past hour or two trying to find the solution for this. there's a lot of suggestions out there, most of which revolve around changing the doomconfig.cfg or making a autoexec.cfg. these suggestions didn't work for me and they didn't seem to work for a lot of other people. it seams the steam release (or re-release) screwed those fixes up. however, i did find one solution that worked and i figured i'd share it in case anyone else needed it.
go into /base whereever doom 3 is installed and make a notepad doc. put in the following as you need it, not including the parentheticals: r_mode -1 (means putting into custom mode) r_aspectratio 1 (this changes the aspect ratio 0 is for a 4:3 display, 1 a 16:9 display (widescreen) and 2 a 16:10 display) r_customHeight 768 (means custom resolution height) r_customWidth 1366 (means custom resolution width) r_multiSamples "0" (anti-aliasing) vid_restart
save the doc as res.cfg. DO NOT MAKE DOOMCONFIG.CFG READONLY run doom 3 and bring up the console (ctrl+alt+~ for us keyboard) put in the command: exec res.cfg
at which point the video should restart into whatever resolution you put in. unfortunately, you have to put in the console command everytime you run the game. there are some other command lines you can put into res.cfg to make the game run better. google them if you want them. hope this helps anyone with this problem.