I am experiencing the same with a Canon EOS 7D and EF 100mm 1.2.8 lens. Updated the helicon remote software today, 1 july 2010.
I have been dissapointed with the outcome after using helicon remote automation, and now when I read these posts and checked the movement of the lens during shooting, I realise that this has been the problem: The lens moved half, or less than half the distance it was set to move, while shooting the set number of shots. Typically the top of the bug has been fine, but the feet are still after merging not in focus, becuse the lens never moved as far down as it was suppose to. Also after the series of shots has been done, the lens moves back the COMPLETE distance it was suppose to cover, i.e. further back than the starting point since the lens failed to move downstream the complete distance. This also results in that after the series is taken, the set and saved range from start and end has changed, so if one would start again, without changing any parameters, the series will not be the same but start with the focus way over the bug. maybe this is some clue to solving the bug.
The problem might be related to some bug, that I reported on eralier, that the recalculation of steps or distance after changing either, or with the DOF clalculator, sometimes flips out. E.g. I just set the range which included 36 focusing steps, set the distance per step to 2 focusing steps and recalculated the number of shots: HR gave 2 shots ??!! Aso after showing some of these weird claculations and I start shooting anyway, the numbers suddenly change and it takes a different number of shot than what the box was set at when I pressed run. These things has only occurred sporadically for me so it is a little difficult reporting on them, but I thought anyway to mention them since it might be related to the problem above.