I have experienced this issue with Office 2010 too. It drove me nuts - especially as colleagues thought it was Finger Trouble or other User error when I knew it was not! Eventually, one of them witnessed it by chance when my laptop was connected to a projector. Donk-donk-donk - one by one, about a second apart, my inbox emptied itself to the deleted items folder.
I tried everything from deleting all rules and disabling archiving to running virus and root kit checks to trying the mentioned repair tool - all to no avail.
For a while I lived with it and simply got in the habbit or regularly purging the deleted items folder (or if I was confident, Shift-Deleting to bypass the folder in the knowledge that if I goofed, anything deleting is in fact held on the server anyway for 90 days). This made it easy to simply drag the wanted items back to the inbox without having to search carefully.
In the end I gave up and rebuilt the laptop (in my case easily and quickly done from a system image taken a month before and then by copying my documents from backup). Problem solved - admittedly by somewhat drastic workaround!
The cause remains a mystery beyond establishing that it ONLY happened when connected by WiFi - never by Ethernet.