[Tolkien]

Aha, I know exactly what's the problem. Look in the following file directory:
C:\Users\(insert your user account)\AppData\Local\VirtualStore\Program Files\dominions3\savedgames

On Vista, there is a default security feature that separates user account information, so that if one account were to acquire corrupt files, viruses, or something, it would not be passed on to the other users. Or at least, that's the gist of it.

So yeah, at the present, Vista isn't saving your files to programfiles, but onto a separate folder on your account. You can turn this security feature off and have it save directly into programfiles, but I forgot how to do so.