I'm having this problem as well.
Mac OSX 10.7, Mac Mini, using a Cupcake CNC. The motherboard is rev 1.2, v2.2 extruder controller, all upgraded to firmware 3.0. I'm using ReplicatorG version 29. Note that the preferences do not update or work for temperature control, either: when I ask the machine to warm up, it will only warm up to 75 deg C. If I change the value in the preferences, nothing happens (when pressing tab or enter). When I exit, the value (say, of 160 degrees) does not save after shutting down RepG. That is, I re-open RepG, and the value of 75 is in the preferences still.
I downloaded ReplicatorG on a Windows XP VM, installed the virtual serial port drivers, and could not get a control panel. I was able to get the machine to heat to 160 degrees through the preferences (those seem to work in the Windows version), but the control panel will still not come up.
I do not have a Linux VM to hand on this particular machine, but will download Ubuntu 10.04 and give things a go there.
I'm happy to try and help debug this further; my username at gmail will reach me. We'd like to get our Cupcake up and running, and are glad to help answer questions/document solutions as we go.
Cheers,
Matt