Update: Still does it even with a new raid hard drive system and Kona card. CS4 has some issues. Looks like it has a hard time with a segment over an hour. Answering my own posts is getting kind of old. But at least I don't tell myself they are dumb questions.
what's your footage, and what's the project settings you have in play?
are you saying there's no difficulty editing the same footage that's less than an hour? how does your system behave with SD footage?