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Unfortunately, I can't give you specifics as to why, other than an intermittent signal loss, or system confusion somewhere. I would troubleshoot the "brain" and see if there is a reset setting or something you may have missed. There could also be some sort of current from the stock system (if still on board) running through it's system checks.
There is a reasonably amount of info out there that an aftermarket system is a total nightmare due to the complexity of the stock alarm/security system. This even goes as far as not installing an aftermarket stereo to a degree.
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