There was a change in DQMH 5.0. The numbers start now at 1 instead of 4001 and they continue to increment. The way you do know that the module does stop is that the library for the clone is not locked after you stop the API Tester.
There is more explanations about this change in the first VI in the lower left of the Main.vi. You can choose to change the boolean input to destroy the reference in exit and that will be the same behavior as before. However, that leaves your program succeptible to root loop issues.
Check the video of the presentation Joerg and I gave at VI week, we show there what the root loop issue was and how DQMH 5.0 fixes it.