I can't be exact since I'm not sure what to look for, but you should perhaps compare original non-fglrx xorg.conf that worked (from what I understand) and the one fglrx generated.
What I always do is just use my original xorg.conf without generating it by fglrx and change the Driver (under graphics card device) from "ati" to "fglrx". You might check if it works for you.
Hope it helps a bit
