Les,
I do not have much experience on the SMC jack system since both of my Beavers came with HWH jacks, but a bent shaft will cause a jack to bind when retracting. On the question about the indicator light, there are three possible types of indicator switches. They could use either a mechanical contact switch (push button), a magnetic proximity sensor (like most HWH systems), or a pressure sensor. If either of the first two are used, a jack with a bent shaft should not indicate "fully retracted" until it is fully retracted, but if a pressure sensor is used, the jack will show a "fully retracted" indication if the jack binds from the bent shaft before full retraction.
If the indicator works properly when the jacks are extended, then you either have pressure switches or the one jack has an inoperative sensor. You will need to do some trouble shooting to determine exactly what your problem is.
Gerald