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...brief spurts of activity in the drive train before a return to silence ...
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Do you get any repeating errors in your Diagnostics tab? Do you have any vision code running on your cRio?
This sounds like the lag our team gets sometimes. Check your DS Charts tab and look at the CPU usage of your cRio and the packets being lost. A lot of times, we get "brief spurts" whenever our CPU is pegged at 100%, which can be caused by anything from vision code to error messages.