Mike,
To rule out the possibility of this being a hardware problem in the FP-CTR-500 module, you can swap both of your FP-CTR-500 modules. I suspect that the problem will remain on the same signal/channel indicating that it is most likely a signal problem.
You may be receiving a double count as a result of noise or signal differences in the sensors wired to the various channels. To reduce the likelihood of a spurious signal causing a double count, you can enable the low pass filter on the FP-CTR-500 to reject signals above 200 Hz. If you look at the signal on a scope, you may see that it is fairly noisy and could use some filtering. Also, consider if one sensor has a longer cable run then the other or if it routes near something that may be electricall
y noisy.
Regards,
Aaron
LabVIEW Champion, CLA, CPI