usmarinedelta

...

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One fob is the original keyless entry fob, while the other was supplied with the alarm, intended to
replace the original.
The keyless fob communicates directly with the keyless entry module, but can't control the alarm.
The alarm fob communicates with the alarm module, which in turn sends a hard-wired signal to the
keyless entry module to unlock/lock the doors.
I suspect that whatever mod you did tricks the keyless module into thinking the ignition key is
not in, but that had no effect on the alarm module. You'd need to do the same to the alarm module,
but that could have unintended consequences depending on how else the alarm uses that info.

If your goal is simply to use the power locks while driving, and it doesn't have to be with the
fob, Modifry has some tricks.