For starters I am using this GREAT answer to achieve custom post types as well as a custom way to insert those post types into other pages, you can view that answer here: Custom field/meta populated by dropdown of existing posts?
I am running into a problem however when wordpress auto saves itself, it clears whatever metadata i have put into the forms.
I select the 3 drop downs I want from my metabox and hit update.
The page reloads and the 3 choices are still selected. In phpMyAdmin i can look up the metadata and see the array in place as it should be.
I now wait for wordpress to auto save.
As soon as this happens i can either refresh the page (not update, just refresh) and the metadata is lost, or i can look up the metadata in phpMyAdmin and it will display nothing (ie: its gone).
I'm guessing that this has something to do with needing to tie into another hook (some sorta auto update hook) or something, but even then it doesn't make sense that it would actually delete your metadata (rather than just not auto updating it).
Last note: If you copy and paste Mikes code into functions.php, you should be able to recreate my error (in wordpress 3.1) very easy.