I'm not sure if it has anything to do with the fact that I use ALZip to manage my ZIP files, but any time I delete a file in a ZIP archive located on the desktop, the ZIP archive dissapears. (At least I know how to get to the actual desktop folder, as I can access the "invisable" ZIP file that way.) ALZip automaticly saves the ZIP archive whenever any changes are made to it, so that might have something to do with it. The "disappearing act" only happens when I delete files from the archive, not when I add them.
I can get it to re-appear by moving the ZIP to another folder (accessing it via the desktop folder) and then back again. Even after that, though, it still disappears any time I delete a file from the archive. Hopefully this problem can be addressed in the next release.