If when you shut the tractor off she draws heavy discharge amps, the Cutout Relay (one of the relays inside the VR) may be stuck/burned closed. Kept that way the battery will rapidly discharge plus the genny can get hot....
If you remove or loosen the generators belt and the genny spins when you shut down, thats most likely the problem. If shes turning (motoring) if you remove the wire on the VR's BAT terminal (or GEN/ARM for that matter) that will obviously stop the discharge.
If you happened to change the battery polarity and failed to Polarize the genny before start up, such can damage a VR ya know???????