God I hate trouble shooting mobos/systems. I used to work for a GFX chip company sitting there trying to figure out what was wrong had to be one of the most annoying things in my life.
however, a couple of things may help others help you:
1. what OS are you running?
2. after the long boot process did you run any type of diagnostic software that may help narrow down or even pin-point issues affecting the boot process?
i think it is specific to XP but not totally sure. also, it mentions an app called Bootvis which is no longer offered by Msft. you can, however, google it and find it elsewhere (free).
if it is XP you can run Msconfig and see what's going on in your startup config. you may have some rogue app mucking it up for you. i think the above link also mentions msconfig.