Chris - did you get this professionally installed?
If you click on ChrisD's name and hit "show all user's posts", you'll see his comments about the installation. There were a few people working on it. I think there's even a photo gallery documenting what they did.
Chris, when you get the replacement unit, make sure to put in the new sled, too. Don't just plug the Empeg into the old sled, install the new sled. The problems you've described sound like wiring issues, and installing the new sled is the first step in eliminating the problems.
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Tony Fabris