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Sounds like an intermittent connection upstream of the ignition switch and the Keyless entry module. One likely place is fusible link E, which is one of the links on the terminal post on top of the passenger side wheelhouse next to the battery. Does anything in the gauge cluster flicker also?
 

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The easiest and probably best test is to just move the link(s) and wire(s) around while the ignition is on and notice if the locks operate by themselves or the engine stops.
 

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All right. let's try another tack. I have a feeling that if you monitor the voltage at the fuses, you can narrow this down. I would measure the Gages and Courtesy fuse voltages (not at the same time) while this is happening and see if the 12v drops out there. The Gages fuse carries the ignition voltage to the Remote wireless entry. The Courtesy fuse carries current to the Remote wireless entry, and is on the same circuit as the PCM battery power. If those don't show anything, I would try measuring at other fuses. They are a convenient place to monitor circuits. If you find one that drops out, this can help trace the problem. Good luck.
 
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