Ok, now the big question: how to reproduce it? If you close UAPP by using the back button and then do a close all from the recent apps list, how do you get to the situation where there are multiple UAPP's in the list?
OK, there's one way of doing it (Android 4.2.2, tested multiple times). With "Recent apps" empty and no DAC connected, launch UAPP. Close it (with back button). Check "Recent apps" - one "instance", so far so good. Now connect DAC. DAC gets detected, UAPP launches automatically and now you see 2 UAPP "instances" in recent apps list.
Aha! Thanks for finding that out! So Android probably thinks that it is a different app when it automatically starts it. I'll check if there is something that can be done about it.