Do you have any sensors attached to your system telling something about the movement of the motor? If you are monitoring those it could well be that the electromagnetic field of either the motor or the relais which drive them disturb either your program or the sensors.
I can speak from experience, I had a system counting pulses over 25 meters at about 700 pulses per meter. Also a 3-phase 380V motor going left and right and in two different speeds. Everytime the distance was run the pulse-count was different (on my controllerboard). Then I built an external counter with CD4029 etc and it worked perfectly!!! Only 1 pulse difference per run. About 17,320 pulses each time. I went nuts.
Finally, desperately I changed the input on my application (TTL) to the same I had built in my counter (transistors BC337) and problem solved.
The relays, together with the motor caused many spikes that influenced the working of the application.
Hope this is of some help.

Aad Sieraad