This problem sounds related to issue 7 (
http://code.google.com/p/autoandroid/issues/detail?id=7 ). In both
cases positron doesn't know how to properly kill an app to restart it.
It can shut down all its activities, but the hosting process (and
apparently some global UI state) will survive. I doubt triggering a
garbage collection in the device would help much, but it might be
worth a try.
If instead you want to disable exiting the app after every test, take
a look at the unit test super class:
http://code.google.com/p/autoandroid/source/browse/trunk/positron/src/main/java/com/googlecode/autoandroid/positron/junit4/TestCase.java
That super class is fairly dumb, on purpose. It creates a
PositronClient which will deal with talking to the instrumentation on
the device, and delegates a bunch of convenience calls to it. It also
(line 25) declares an @After tearDown() which calls finishAll(). This
finishAll() call is what (fails to completely) kill the app. You
should be able to easily override the method or swap in your own test
super class (or abandon junit altogether if you have the itch.)