Adaptive clearing toolpath bug

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Hello,
I'm experiencing an issue when running an adaptive clearing toolpath. I don't understand exactly what the problem is, but I have seen it across different models and different files.
When running an adaptive clearing toolpath, the machine takes a series of fine step-downs, a roughing pass, then another series of fine step-downs and so on.
The error I experience is that the roughing pass cuts into the area machined by the fine step-downs above it. It cuts the right shape at the wrong place, as if the zero moved when it began the roughing pass. Needles to say, the tool isn't behaving the way it looks in the simulation
Has anyone else experienced an issue like this? Anyone found a solution? If anyone has suggestions I'm ready to test them and report back with results.
Technical info:
The machine is a shopbot buddy, the computer runs shopbot 3.8.62. The controller box firmware is 218. Post processing set to Shopbot openSPB
A clue:
I examined the gcode lines before the error occurs and noticed it was the only time it used J3 instead of M3. The shopbot cheat sheet mentions that J3 can be calculated in either absolute distance (SA) or relative distance (SR). Maybe this explains the "moving zero"