I think I understand what's causing this. Alt is the windows shortcut for the top menu. In most Windows programs, doing an alt-tab does not engage the top menu shortcut. But in AD, the top menu shortcut is engaged w/ an alt-tab.
Also, unlike other windows program, the top menu is STILL engaged when the user comes back to AD. Therefore if someone switches back to AD after an alt-tab, AD still thinks the user is still on the top menu (you'll see the top menu items underlined).
Therefore, the workaround seems to be to press alt until the top menu items are no longer underlined, or to use another keyboard shortcut to switch between programs (either Win-(# of program you want to select) or Win-tab).
I would still consider this a bug and hope this can be corrected in a future release.