Counter is skipping counts

I am using a GPCTR with NIDAQ 6.9.3 on a MIO-16XE-50. I have a motor with a sensor on it that sends a digital pulse based on revolutions. I am using VB6.0 to watch this counter and using it to trigger data conversions. Intermittently, that is, with no pattern or consistency, the counter will skip counts. I know the VB loop isn't too slow, and I've tried slowing the motor down. Any idea as to what is causing this to happen? I've tried adding a low-pass filter to the signal, thinking it was glitchy, but that didn't help.
any ideas or help would be greatly appreciated.

Is there any buffering between your sensor and the 16-XE-50? I have noticed that these cards do not behave well if the source impedence is high. You should put a Schmitt trigger between your motor signal and the card. I assume you have checked things like switching levels to make sure your signal is switching a full 0-5V or close to it. I have done a fair bit of work with the GPCTR's on that card and will help further if you need it.
Regards
Jamie

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