Measuring capacitors with a multimeter set to measure resistance can give some interesting results, especially depending on how your multimeter operates. Capacitors react rather differently to AC, and many multimeters can actually apply a pulsed signal which is AC-enough to cause stuff you might not expect. You need a much fancier device in order to measure ESR (equivalent series resistance) in a capacitor, and to get a trustworthy result you really want to disconnect it from the circuit.
That original controller looks spotless, and they are pretty damned robust so I hope it works out for you
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