Hi HFoletto,
Following along here since you have checked your source with another amp that eliminates the source. Tubes switched sides and still the same problem would eliminate the tubes.
Try moving your headphone plug around in the jack while it's plugged in and see if it is the headphone socket. Grab the plug and apply a little sideways force to it, up down left and right to see if the sound comes back.
I have the MK IV not SE and had to change my headphone jack since the non SE versions are really cheap clone Neutrik Jacks.
Other than that I would guess there is a component bad on your board, or the volume pot going bad.
Those little gain switches might have some dirt / corrosion on the contacts as well, so take a little screwdriver and move the switches back and forth a half a dozen times to clear the debris if any.
Also could possibly be a dirty socket hole on the driver / power tube sockets you might want to try a piece of wire just a hair bigger than the tube pins and go in and out of each socket hole a few times to clean them.
Do all of the above with the power cord UNPLUGGED and the amp left for a few minutes to discharge the capacitors inside.
These are the things I would try, and hopefully it is just the headphone jack which is very easy to clean (Q-Tip with contact Cleaner) or if you have to change it only requires some basic soldering skills or a friend who solders.
Good Luck and let us know how things turn out.