What charger and what kind of stereo? Stereo running on an inverter or is it a 12 Volt unit? Any mega amps or subs in the system?
Sounds like the charger is not doing much, Mark. Measure the battery voltage at the battery posts (not clamps or terminals) with everything off.. charger, master DC switch , DC main, and all DC branch circuits. Turn the charger ON and re-measure .. you should see a rise in voltage to above 13 volts if the charger is working and the terminals/connections are clean. IF you don't see that, check any fuses or breakers in the charger and check to see if it is getting 120 volts at its input. Now turn on the DC master and measure the DC volts at the panel as you turn on each circuit that was on when batts went south. The volts should stay above 13.5 or so.. The first thing that you turn on that pulls the volts below that is the culprit. I know this isn't easy because your batts are in "the pit" like mine are.. easier with two folks and be careful if you measure on the back of the panel to not get into the 120V stuff.