First, I'd make sure the headphones are good and there is no short in the headphone jack. Try removing the headphones and see if the speaker sounds the same. But, my guess is that the pot for the threshold is dirty. If the machine is no longer under warranty it's always a good idea to clean all your switches and pots with some electrical cleaner first before sending it in somewhere. I bet 9 times out of 10 a problem with a Sovereign is just a dirty switch or pot. That's one of the big drawbacks to hip mounting because any dirt or sand on your hand falls down and sits right on the face plate.
While I'm at it, who has a good cheap source for those rubber boot switches? I'm guessing an electronic parts store would be much cheaper than buying them from a Sunray or Minelab dealer but I don't know what size they are off hand. Anybody have a link?
Don't use WD-40 or anything else to clean pots or switches. Pick up a good electrical contact cleaner from Radio Shack or Home Depot. You want the type that doesn't leave any lubrication or residue. Most of the time you won't even need to remove the switch. Just spray it into the toggle's opening. Pots can be tricky but some times it's possible to do it with them as well without needing to get inside to access it better. In RC a lot of servos go bad because the pot has dirt or carbon built up in it. I've salvaged a whole pile of servos by cleaning the pots on them, but I took those pots completely apart do clean them properly. Still, most of the time you can get some spray in there just by getting near the dial shaft and forcing it in.
In a pinch on something I don't care much about like the old boom box in my garage, you can use WD40 to clean switches and such. It's probably OK for switches but the reason why it's a bad idea for pots or sliding controls (such as volume/balance/etc on this boom box) is it will leave an oil residue which can do funky things to pots in the long run. Pots and sliding switches have a surface that little "feelers" move across and change the resistance or other factors in the circuit. That's how a volume control works in a basic sense.
Anyway, for years the volume control slider on that box had a dead spot. It would drive me crazy trying to get the volume right without hitting the dead spot which would kill it or cause static. Finaly wasted a few seconds out of my life to pick up a can of WD40 and spray it into that slider. Problem gone. Always amazes me how I'll avoid something and let it bother me for years when it only takes a minute or two to fix.
Almost forgot- Be careful with getting any spray on the face plate or plastic. Some contact cleaners will melt plastic, so don't fire hose a whole bunch of that stuff into the inside of the switch/pot either in case it drips into the box.