The jumper is just two solder flowed points inside the PCM.
I don't see those ever "unsoldering" themselves without killing or damaging the PCM. (sustained voltage spike or the like)
Now a kill switch hooked to the PCM input/output off the coil pack may cause suck a voltage spike. (the PCM works with milliamps or less!!!)
Especially if it was unshielded. (i.e. highly prone to shorting from water!

)
I would go find who did this other electronic installation and ask WTF they did and why they did it so piss poor!!!
Until proven otherwise I would "assume" it's from this added on shtuff and how it was done.
The alarm/timer setup didn't mess with the PATS system at all did it? Like splicing wires or??? Another place for shorts...
I know if the installer of the TT didn't follow Stazi's write up that will cause problems. I know he ran across a few but don't remember what they were off hand.
That's yet ANOTHER part that is tied into the ignition system somewhere...