I’ve been having this bug for a while now (maybe since ever)
1. Open project
2. Change in scene X
3. Save (CTRL+S)
4. ... Unity crash at some point
5. Open project
6. The save at step 3 seems to never occurred
7. Repeat step 2
8. Save
9. Exit Unity
10. Open project
11. Save at step 8 worked
12. ... Unity crash
13. Open project
14. Save at step 8 is still working
Why does the “Save” only work if Unity3d exit safely? Since Unity does crash a lot (Windows 7 Pro x64, Unity3D 3.3.0f4), I’m running out of patience…
Edit: It’s not the crashes that are the problem here, it’s the save/recovery that is weird/buggy
Maybe try saving it as another scene file. Am using 3.3.0f4 and win 7 x64 myself and the crash is not as constant as for mine. But one thing i noticed for me is that, it crashed if i am playing and editing the scripts. It will sometimes crash it and amongst other stuff.