I had the same problem with my project. I had about 11 sequences in 1 project so i split it into four project files just to be on the safe side each containing 2, 3 or 4 sequences (will be adding a few more).
Now to get a full compile what i do is i render the individual sequences into uncompressed Microsoft Avi files, then i have one new project file in which i line up all the AVIs behind each other then export that as a fullblown .avi
Then i encode it into XViD or X264 using Virtualdub. A bit laborious but it does the trick for me so far (knock on wood).
My project file was only 10megs but it heavily still image based so lots of those in there. And i dont know what kind of machines u guys have, i’ve got 2 gigs of RAM.
Hope this helps if it becomes a problem again!