i had similar problem with my softlimit on my fresh lathe retrofit,
my soft limits works very good, it stop good on both axis but when i try to run program, mach3 send messagebox warning if my program run within 4 inch of the soft limit ....
if i escape the alarm, the program run good without close position with limit
i have only .75inch of slowzone in soft/home screen, this lathe run on diameter mode, i use smoothstepper
tanks
fred