[Brian]

Everyone that's having this, can you do the following:

Move all your actions into one of the Miscellaneous projects.
Delete all the empty miscellaneous projects.
In the Data pane of preferences, make sure your "Default list for single actions" pop-up reads "Miscellaneous". If it reads, "Create when next needed", set it to Miscellaneous.

You should have to do this, at most, once on each machine you sync on. That should clear the problem up, though, and it shouldn't come back.