I haven't had this specific problem, but I did have some pretty major ground loop issues when I first setup my Mark IV rig. I would get loops between the amp and G-major, and also between the amp and pedalboard.
Then I picked up one of these (Ebtech Hum Eliminator) and all my problems went away:
http://www.audiomidi.com/common/cfm/...Product_ID=314
$60 sounded like a lot to me at first, but once I tried it, I kicked myself for having not purchased it sooner.
--B