I know, that's the same in 1.02, I discovered the bug. It was fixed in RC4 but from RC4 the updates became very unstable again. If you've got problems with RCfinal you most likely are going to have problems with any build above RC2. From RC4 some fundamental changes were made.
Which ever version you choose, it's never a win win situation. So the best is to wait for Lee to release another update or just stick with V1.0 as some have done.
If you use 1.04RC2, you could just give the player a notice to save at the start of the level to ensure the best results.