I’m sure a member of staff (Edwin? when he was still with the firm) answered a question about this issue and replied that it was a limitation of the simulation only and the toolpath would be generated correctly. I used your file with a huge stepdown to simplify the tool path and got this result:
… just showing the head. The simulation was showing exactly what you posted.
Incedentaly, the version of SMLuban 3.15.1 does not refresh the simulation image correctly after chaging the toolpath, I find that clicking the ‘eyball’ on the toolpath off and on fixes that problem.