Trouble shoot.
(1.) Do an extensive visual check of all track involved. A lot of times something has fallen off and is causing the short. Also look for black burn marks that may indicate unusual electrical activity.
(2.) Disconnect all wires from the transformer. Turn the transformer on and check each track circuit. That should eliminate a transformer problem.
After re-attaching track to transformer leads.
(3.) A two handle transformer check one then the other. That should eliminate 1/2 of the area to look for a problem.
(4.) Work from primary terminal strips to different track areas. Eventually you should determine the short/fault area.
(5.) Worst case you end up tearing the track apart, but do it systematically. Example: split a loop in half, then quarters, etc. testing each isolated section for the short/fault.
Best wishes
Mike CT