Ok, I'm running HJ v297, software 2.00 b13 developer image. I have nothing in my preinit.d except M50gpsapp.
I always use the rotary knob to access HJ, using the remote doesn't fix it though.
I found out that I don't need to have a gps receiver connected. I even don't need to leave the HJ menu! I just do the following:

1. I enter HJ, starting GPS
2. The screen show 'waiting for gps location'
3. I push the top button to return to the HJ menu
4. I select GPS again.

The sound output pauses for a short moment, and then the empeg changes the sources rapidly between aux and player.
Again: No gps receiver connected, no one sitting on the remote ;-)
I've noticed that this happens quite randomly. It's not 100% reproducible as I first stated. Maybe it is related to 'restore visuals: enabled' in HJ?
I've also noticed that I can return to the HJ menu while the player is switching by pressing the rotary control. As dbrashear already told, the GPS menu item has gone then.