Senseiweasel: I can confirm that this fixes all the save game bugs (disappearing monsters and loot, inablility to overwrite etc) - unfortunately as it uses a totally different set of saved games you will be forced to restart.
It does fix all the issues, but you're wrong on having to start over. No need to worry about modified game files either.
Your pre-fix save games and settings are located in*:
C:\Users\%USERNAME%\AppData\Local\VirtualStore\Program Files (x86)\GOG.com\Vampire The Masquerade - Redemption
You can copy the above path into your file explorer's location field. It will take you to the correct folder automagically.
Just copy the SaveGames folder and the masquerade.ini file to the installation folder*:
C:\Program Files (x86)\GOG.com\Vampire The Masquerade - Redemption
Now run the game as Administrator and it will behave correctly.
*assuming Win7 64bit and default installation options
EDIT: To clarify: I did not have to mess with the folder properties or change anything else. Just follow the above steps and save games will be overwritable and earlier saves (or starting over) will behave correctly.
EDIT2:
Fasckira: FYI (to those who find the issue persists after trying the above); if you find indexing is already enabled and its still not working, disable it then re-enable it on the folder. This was the last piece I had to do to get the save games working.
System: Win7 64
lordhoff: I find this interesting as it seems to be isolated to certain people. I've played the game dozens of times with both bought CD and GOG with XP Pro 32 bit, SP3 and didn't even know how to run as administrator and never had a save-game problem. Makes me think it might actually be more of a virus protection suite problem.
The Windows 7 issues seem to be related to how VirtualStore works (it seems to be a Windows 7 feature, so it probably won't affect earlier versions of Windows). VirtualStore seems to redirect hard disk access to certain folders to a folder inside your user directory. VtM probably makes assumptions that are no longer correct with VirtualStore in place and goes wonky.
Enabling indexing on the game folder seems to solve the issues in older versions of Windows, but Windows 7 with VirtualStore requires running the game as Administrator (and moving the pre-fix save games) unless there is a way to disable it.