As far as I know, whenever Blender saves a file, it first stores it under “.blend@” and then renames it to “.blend” (maybe deletes the “.blend” file first). In this way, when something unexpected happens during the saving, the “.blend” file is not destroyed.
Most likely, something is interfering with the renaming. Do you use something like Dropbox or another backup solution for this folder which might not be happy about what Blender is doing?
Edit: This thread might be useful: