Saving is not your issue.
I think loading the QAT items again is your problem.
The code which loads the QAT items looks at the logical tree of the Ribbon and i think your items are not part of the logical tree when the ribbon is loaded.
However, i made the LoadState method of the Ribbon public with commit http://fluent.codeplex.com/SourceControl/changeset/c8a2166cb3ee you can use this method to (re)load
the Ribbon state (which includes loading the QAT items) later, when you added your ribbon elements/groups to the logical tree of the ribbon.
Can you try this and tell me if it worked?