(Sorry, I didn't really read this - just saw the OP mentioning nexerelin and moved it to this subforum.)
As best as I can tell, this kind of error is some kind of disk write issue. I'm not familiar with the gory details, but the game tries to verify the saves are written out correctly (ofc it can't verify every single thing, but for example it checks for that "bunch of NULL characters" issue, and despite that, those files can still get output), and *to the game* it looks like the files got written out fine, but it's not actually fine on the file system. So I suspect it's some kind of issue where there's an OS caching layer and that OS write cache does not actually make it to the disk. But when the game reads it back while it's still running it looks fine because it's seeing the cache, not what's actually on disk.
I'm not super sure what to actually suggest here. Using Java 8 (or Java 23, using Himemiko's conversion kit) may resolve the issue - not for any specific reason, though. Another thing that might be worth a try - if you have multiple hard drives or partitions, running the game off a different one.
Also, if there's other software running - or perhaps an antivirus - it's possible something is messing with the game, but it's just hard to say, unfortunately!