I'm trying to export a 90-minute timeline "using current settings" to a QuickTime file. It exports fine, is 13GB when complete, but during playback starting around 10 minutes into the movie it seems to drop a frame or two every few seconds, followed by the whole audio being out of sync. By the end, the audio is way off.

Has anyone had this problem? Am I asking too much to export the 90-minute movie in one self-contained file?

Specs:
MacPro running Final Cut Pro 6
HDV video 1280x720, 720p at 23.98fps

I may have done my math wrong, but 13 GB seems way too small for a 90 min movie in 720p. What are your settings? Have you rendered your timeline?

Prior to exporting did you Mixdown your audio?

My settings are:

Preset HDV - 720p24, audio 48KHz 16-bit

Yes, I have rendered my timeline, and have rendered the Mixdown. I'm using "Current Settings", self-contained and am not re-rendering.

I had an error just like that (the audio part) a long time ago. I think I ended up figuring out it was an error with 30fps (non-drop frame) and 29.97fps drop-frame. In other words, the audio was running slightly slower than the video and became apparent over an hour.
Might apply in your case, too, but with 24/23.96.

As for not re-rendering... try it. Might help. Who knows.
As for self-contained... try turning it off. If it works, then use quicktime pro (free with FCP if you haven't used that already) to resave as a self contained movie. (File>Save As...>etc, check "self contained")