Ah, yes. If ground bounce on a state change is the culprit, that makes sense, thanks.
(Also, thinking about it, if OP's doing an encoder 'properly', he should be immune to all this, since it's just a (slightly annoying) case of rocking back and forth across a single encoder edge - the decoder, whatever it is, shouldn't count that as a succession of pulses, without seeing a transition on the other channel...)