I run Org from the git repo, updating daily.  I unsuccessfully tried syncing with MobileOrg (Android) about two hours ago.  I reverted org-mobile.el back to the version from yesterday and found the problem: TODO keywords aren't being listed correctly.  Here's an example:

Old:
#+TODO: TODO | DEFERRED DONE PENDING CANCELLED

New:
#+TODO: TODO

    This messes with MobileOrg, preventing it from syncing.

    I worked through the problem, which appears to be caused by org-delete-all being called before the TODO keywords are inserted into the file.  I attached a patch that fixes this problem.

-- 
Ian Dunn