Other possible sources include a bad bullet in the system or a failed antenna (possibly a bad bayor a bad interbay line).
Troubleshooting this requires an engineer experienced in FM transmission systems equipped with, at a minimum, a TDR. He should be able to determine the approximate locatation of the fault, and your tower crew can then examine the problem area.
Among the tools that I sometimes use when tackling such problems are a VHF bridge with generator and detector, a shorting termination, a small dummy load and a wattmeter (both large enough to handle the exciter) that can be hauled up the tower, and a transition to connect the termination, wattmeter or dummy to the top of the transmission line.