My bios doesn't have "AGP turbo mode" option, could it be called something else? The graphics are actually not slow or jammed at all. After starting X everything works fine, it's just X startup that takes forever, so I doubt that that would help.
The delay is the same in both cases, when X is started by going to runlevel 5 or started with startx command from runlevel 3. Unfortunately I'm not able to use other machines to ssh to my own, so top really is pretty much out of the question. Unless ofcourse there is some kind of "logging" variant of top that shows what processes were run during X startup and how much they consumed time.