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I managed to 'resolve' the issue by flipping the wiring of the encoder that was giving the opposite readings. This is not a full solution, as now I believe I have that encoder technically wired backwards, but it does fix my odometry issue, and now allows Gmapping to construct a reasonable map.

I will update at a later point if I find the root cause of the issue, but this certainly works for now. I'm also not entirely sure how the diff_driver_controller package works, and maybe the way I have my motor mounted I need to account for the flip somewhere. Either way, take away is switching the direction of the encoder readings solved my issue.

For reference, this is my motor controller: https://www.roboteq.com/products/products-brushed-dc-motor-controllers/sdc2160-detail