@andyvirus I stumbled across this thread with a similar issue to yours. I figured I'd reply in case anyone else finds this thread looking for a solution. I fixed my issue by removing any "T" commands from my Tpost/Tfree/TPre macros. I had a T-1 in the beginning of a few of them and I believe this was causing my G-code for lowering the bed to be run twice.
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RE: Z Height at Start or Tool Change