You have not been using the Warp Stabilizer on a number of clips have you? If so, that could be your problem. Data for the stabilization is stored in the project file and this increases in size rapidly if much use is made of the stabilizer.
My work-around is to export each stabilized clip using a "lossless" codec, and then import the intermediate clip to replace the original with the stabilizer effect.
No. The issue was resolved by updating to CS6.0.2. Unfortunately that only fixes the "save" bug. The project took over 2 hours to open, but once opened, I could re-save it to a 1.9 Mb file.