That's very odd indeed.
Could you upload to me an example troubled GuildRaidSnapShot.lua file (the ones you're uploading)
Have you noticed any system to the problem (ie, only certain bosses are missing, all snapshots after/before a certain time are missing)?
Try typing "/console reloadui" after each boss's loot is handed out. This ensures that the data gets written to the hard drive.
Also, WoW isn't crashing or anything is it?
Also, you're not typing "/grss reset" during the raid are you?
Keep in mind I'm just tossing out a lot of ideas to try to solve this, as I'm not sure the cause.
1) sure, I'll send a file right away....
2) I started doing a reloadui after every bosskill, problem is still there.
3) Wow crashed once, but in a different raid, it didnt... and problem was still there.
4) tried GRSS reset before we begin the raid.. just to try to clear everything, problem still there.
Im at a loss as to what is going on... will submit that file in a few min...