Had a similar problem with my Pirates. Check the connections on the Trough opto board. If they seem good go into switch test and slap the cabinet a bunch of times, hard, in different places, see if any switches register, then see if the trough jam switch registers as well. If so check to make sure there is nothing shorting/loose on the switch in question, then manually close the switch and see if the trough jam switch closes with it. If it does the trough opto board set is faulty. If you just bought this machine NIB then its still under warranty, if you bought it second hand there is no more warranty.
http://www.marcospecialties.com/pinball-parts/515-0173-00. This is for the transmitter, the receiver is out of stock, but you maybe able to find one somewhere else, or back order it.