On the left: Crate that hasn't been rotated so the axis of the lid hinge changes from X to Y nor vise versa.

On the right: Crate that has been rotated so the axis of the lid hinge changes from X to Y (same with vise versa)

Here are the settings for the lid:

If I change it to orientated instead of fixed, whenever the lid opens it clips then snaps off.

Thanks in advance for the help (:

Can you export the structure, so I can test it myself?

This one. The textures require Biomes o Plenty. I was able to reproduce the issue by rotating an mirroring it. At certain rotations, the lid inverts the rotation and rotates inwards.

crate.txt

Fixed in the newest version, unfortunately the code was executed in the wrong order which caused this issue to happen.