Is the blower connected to organ windchests, or for now just blowing
into free air?  Blowers running wide open in free air draw tremendous
extra power, and your Allen-Bradley starter control may be reacting
correctly to this overload and shutting it down.

Try taping some cardboard over the blower's intake so no air can pass,
and see if it now runs longer.  If this fixes the problem, then you
have to hope that, once everything is trunked together, the blower can
fill up your organ's reservoirs before the controller cuts it out.
Perhaps it is adjustable.

Mike Knudsen