Your Univolt converter/charger may not be working. Check the circuit breaker for it to be sure it is on, or whatever control it may have. I am not familiar with the newer cutter busses.
If the Univolt is operating, it should be humming. Again, I am assuming the 96's still used the old Univolt system.
If it is getting 120 volt power, and is not putting out charge current to the batteries, you could have a blown 12 volt
fuse in the charge circuit. Or the unit itself may be dead.
When you start the engine, the alternator takes over the charging of the batteries, which is why the brightness of the lights came up to normal.
If you checked the battery status on the monitor when the engine was running it only told you that the alternator was working to charge the batteries. BTW, the battery monitors are only a very gross indicator of the actual battery condition.
So, a few things to ponder and check.