Okay, here is my problem. So far none of my other computer savvy friends have found a good answer. Basically what is happening is that I delete a file, and it re-appears, kinda. This isn't an issue with a system regenerating something (like the default music folder), and it has happened with files that could not have been in use with another program. So far I think it has only happened with audio files. When I say it reappears, it only does so in skeleton form. Basically the file shows up, has the properties of the file, and I can't edit it in any way or play it. The shell of the file is there, but there is actually no contents, which have been deleted.
Any clue what might be causing this? So far the only way to deal with the semi-regular issue is to restart that computer and that gets old quick when I'm working with tons of audio files and it happens every few minutes.