The joint orient tool in Maya 2025.3 doesn’t correctly orient the secondary axis to the secondary axis world orientation that you select if ‘auto orient secondary axis’ is selected. Turn it off, and it orients correctly.
Am I missing something?
Maya’s native rigging tools are never the best. I would recommend using these scripts for this task: www.comet-cartoons.com - Michael Comet's Homepage - Maya Downloads
Specifically CometJointOrient. This tool is my go to for joint orientations.
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