For some reason, I just noticed Laura's post on 8-8. It was posted before I posted on 8-6... not sure how that happened.
In any case, the DAQ is software timed, but that's okay. As long as the measurements correspond to the appropriate encoder count, the VI works fine. So far, I haven't noticed a problem with this.
A guy from NI came a couple weeks ago to take a look at the code, and he couldn't find a reason for the behavior. I rewrote a chunk of the code without using the DAQ Assistant, but it didn't seem to matter.
The same guy came back today and we kept testing the setup. Eventually we narrowed it down to the MX driver set, and have submitted the drivers and offending code to NI to get it checked. I'm using version 7.3 of the drivers and 7.5 is posted online. With any luck, the fix is in the newest version.
I'll keep everyone posted. I know you're on the edge of your seat. 🙂