It sounds as though you're getting power only from the isolator system but not from the house battery. Assuming your house battery is charged, this means the connection from the house battery to the rest of the electrical system must have some problem.
Check the terminals and wires carefully, and the connection of the ground wire to the RV chassis. If you have a master fuse at the battery, check that it is not blown. If you only checked the chassis battery for charge, verify the house battery is charged and good as well.
While it probably could be the disconnect switch, I think more often the battery isolator circuit is on the unswitched side of the disconnect solenoid...at least it is on my class C. There are many variations in the wiring, though. If the isolator connects on the load side of the disconnect, then the disconnect itself may well be giving trouble and should be checked out.