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As I'm working on my own EtherCAT slave I was interested in the issue that caused the requirement for a 2ms servo thread to get the stepgens behaving correctly. I mentioned this to someone and they pointed me to a write up by Arthur Ketels where he describes some of the issues related to slaves misbehaving with distributed clocks. I'm not too familiar with this code implementation as it's not my strong suit but I'm curious if you think this could be part of your issue....
https://github.com/OpenEtherCATsociety/SOEM/issues/487
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