I don't have that problem, but then also don't have my lathe setup for homing. I assume you are
using the standard screens of Turn.
Here is something from another post:
"Is it possible to shift the X origin (zero position) to the outer diameter of the starting stock so that
setup operations whether using wizard or LazyTurn G-code are similar? "
Most all programs have X=0 as the origin for their code because it can be a repeatable place to easily
find / reference to, along with a number of other reasons. There are a lot of ways of accomplishing
what you ask. Depends on how "you" want to work and your understanding of Mach3 Turn.
For now here is MY suggestion for when in MACH3Turn:
Zero world X and Z which ( cancels any G54 so there are no offsets ) and set home somewhere away
from the piece, move the tool "controlled point" to where the gcode for the part was created, click part
zero X & Z, ( now machine=program=part cords at the same point ) move the tool to where you want
to start cutting, cycle start the program and all should work just fine. That's a mouth full, but, just one
way of working.
FWIW,
RICH