Ok, I get a tiny thump (pop) as well. Don't know if it's completely 2.0b3 related. This is also at home - I dont have my car install completed to check there.
If I have my amplifier already turned on, plugging in the power to the empeg I will hear a slight pop as the connector begins to touch the contacts - this is before any software gets involved - seems purely electrical.
Then I get a more distinct pop when the empegTux/Rio logo appear (right when the standby light is turning off and the image is popping up).
I tried it right now to verify - because the last few times I've connected, I turned on my amp last and obviously don't hear anything that way.
Bruno