IIRC there are two different community patches to the game, one for Killap's bugfixes and one as part of the restoration project (which includes the other patch) offering additional content. In addition, there was a fairly recent update for them, so if you've downloaded the latest version, chances are that they're different. Make sure you've installed the same version, you might find older versions of them floating on the internet. My advice would be to never delete the Fallout folder of your active game, it will just keep working even if you reinstall your system, Fallout doesn't store anything in the Windows registry, just make sure it's in the same folder or edit the .ini file to point to the new one if you move it.
The other possibility is that your saves are simply corrupted, which can happen, sadly. Although it hasn't happened to me since the community patches, but the official version once corrupted my whole save pool and had to start over. I'm always using rotating saves to avoid corruption, meaning I use all 10 slots in turns, but on this particular occasion I was playing long enough to overwrite all of them in a single session. I could load them back without problems until I closed the game and tried to load them the next day.