I'd take the sub out and look at it. One of my infinitys was doing that and it turned out that one of the wires on the sub had broken loose. It was cutting in and out for a few days and then it just completly broke off. If you're sure your wiring is ok, then it sounds like something is up with the sub.
Also could be the output on the amp itself. Mine is in the shop right now for that very issue.
My passenger side speaker worked no problem, but the driver side cut in and out, and over the course of a couple months would stay off longer and longer until it didn't work at all anymore.
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