I have a 6602 counter card and two encoders. I will eventually have 5 encoders, so as of right now, I have 5 sperate VI's that run simultaneously, echa with its on configured channel and set-up. My encoders have an assumed constant speed of rotation, and my Vi will give me the encoder pulse difference each second.
When encoder channel 0 is turned on, everything is good and the "encoder pulse diference" is relativley constant. then when i turn on channel 1, the count is constant, for about 4 or 5 secondsm and then the count difference goes into a pattern, mid(100), high(190), mid(100), mid(100)low(50), mid, mid, high, mid, mid, low, mid, mid, high, mid, mid, low, ....after some time, it will just stay mid, then go
back into the patter, then stay mid again. sometimes, I can make the mid, high, low pattern stop by opening another process(word, excell, internet, etc).
I have even written a seperate VI tht will read all 5 channels at the same time and i get the same pattern.