I had this problem when I tried installing dropbox on my VPS. I wanted to use dropbox to get a small 1gb backup off of the server, as my puny ADSL would take days to do it, but for whatever reason, after it installed, I noticed on my current PC, 100's of "whatever.file has been deleted" notifications from my dropbox tray icon, and I was nearly dying, thankfully they have a restore option on their site, so I was able to "undelete" the files and save myself from losing so much data...

Seems dropbox really does believe if a file isn't there, it's been deleted.