[whpalmer4]

Well, I've gotten the multiple Miscellaneous folders bit with syncing between two desktop machines, with no iPhone involved. It is possible there is more than one bug here, of course.

At least on the desktop, the program will create a Miscellaneous folder for you if you have the right settings in your preferences. It does this when you have an action in the Inbox with just a context assigned, your clean-up preference says it is okay to clean up items as long as they have at least a context assignment, and the default list for single actions isn't set to something else. Some of these settings (possibly all, I'm not sure) are synced over to the iPhone.

If you do get the multiple Miscellaneous folders, moving all the items into the correct/original folder, deleting the usurper(s), then setting the default single action list to the correct/original folder again (in that order) should get things squared away. I would do an immediate sync at that point.