Thanks everyone for your detailed answers!

I increasingly think there is a problem with the pedal. The reason we haven't changed it yet is that the other pedal is fused into the other crank, and I don't think we have an identical R pedal sitting around, or even another SPD pedal. Of course we could get another one, but while we're at it I think we'll just change the other crank and get two new pedals.

Now: would you give the new setup a chance or would you change all parts NOW to avoid further troubles?