Fixed It!
If in doubt, turn it off and on again!
Not more than 5 minutes after posting here I fixed the issue. I unplugged the stick, uninstalled the CH Control Manager software, restarted and re-installed the stick using the Windows calibration tool. It seems DCS was reading some kind of raw input directly from windows that wasn't going through the CH calibration software.
I'll leave this up for anyone else with the same issue.