Brink, I'm picking up from rferris on the exact same issue and computer. Hope you can still help.
I successfully removed the extra "Alt-Latin #2" entries by removing the AltLatin.dll in System/SysWOW64, then going to the registry and removing the four associated entries. Then I attempted to cleanly install AltLatin again. However, the MSI seems to think it is still installed (gives me options to Repair and Remove), and cannot complete removal--after about 5 seconds from clicking "remove," I get the message that it is "interrupted" and I must try again.
Earlier, when AltLatin was still "installed," it seems that Windows wasn't recognizing it properly because it would be in the list of keyboard layouts, but not show up in the language bar as an option to switch to. Previewing the layout also showed most of the keys to be blank, when it's supposed to be very much like a normal US keyboard until you hit Control, etc.
Thanks for any help you can offer.