hi,
I had the problem with false reading of pulses (when the window of the encoders is almost aligned, any vibration becomes a pulse)
Well, so just modify your software to ignore it. For example, may it help?
1) if a pulse is detected then do not process it as long as there is no next pulse of same direction detected.
2a) If following pulse has the same direction as previous one then process both ones.
2b) if following pulse is at opposite direction then ignore both.
By other words: process not pulses but its sequences: only if two (or free/four etc) pulses have the same direction then accept it.

Regards,
Oleg