I also don't know very much about Scag equipment, but this sounds like a safety interlock problem.
From the Scag owner's manual on page 11:
"The mower is equipped with a safety interlock system
that prevents the engine from starting unless the deck
drive is disengaged, the parking brake is engaged, the
steering control levers are in the neutral position and the
operator is in the seat. The interlock system shuts off
the engine if the operator leaves the seat with the steering
control levers not in the neutral position and/or the cutter
blades engaged and the parking brake not engaged."
There is a contradiction here when the manual says the machine won't start unless the operator is in the seat. Have you been able to start the machine while not in the seat in the past? Most mowers have two safety circuits; one to disable the starter and another to kill the ignition after the motor is running. Most allow the motor to start without being in the operators seat if the parking brake is set.
Here's the manual and the wiring diagram:
http://www.scag.com/OpManuals/STT/2003STTIPL/2003STTIPLcomplete06082.pdf
http://www.scag.com/OpManuals/STT/2003STTOPMAN/2003STTOPMANcomplete03120.pdf