Despite four months of testing, it seems some bugs still slipped through the cracks. A bug was found in which Players who chose a "History" for their character during character creation will lose their keys later in the game when possessing and unpossessing traveling companions.
Recommendation is to avoid using custom histories until the version 1.1 patch is released. If you are playing a game in which you chose a history, you can disable history support in your current game by issuing the following command in console:
G._pcinfo["vhistory"]=-1
It will not however return any lost keys to the PC. You will have to reload a save game if keys appear to be missing.
See this page for instructions on enabling console.