I just upgraded to ATA 3.4.5 and at first was panicked that I had lost all the widgets in my right sidebar. All the default widgets were showing instead. I was getting ready to redo them, when I found that they were hiding in the right inner sidebar, phew

I'm running on Wordpress 2.8.6.

Are you saying the widgets were in the right side bar to start, but now show in the right inner??
I didn't see this with my upgrade.