I program lathes. Very little experience with mills. Woodworking? What's that?
I'm going out on a limb here trying to help, and don't doubt someone will cut it off from under me. But...I'll try anyway.
I modified a v9 mill post for incremental. Boss complained that it wouldn't output incremental now that it is in X3. I checked it out, and the post still said incremental output. Apparently X3 doesn't care what the output is set for in the post. You have to select incremental in each operation where it is desired.
For mills look in the area where the tool depth, approach, etc. is defined. There is a place there to select incremental if that is what you want. I believe this is the solution to your problem. A side note: On a mill or lathe, if you have G54 you will also have G55 through G59 work offsets at a minimum. Hope I used the correct words there (work offsets) else I will get flamed.
Be sure to let us know how you make out. I always like to know "the rest of the story." Too often the OP never lets you know if his problem was solved or not.
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“It stands to reason that where there's sacrifice, there's someone collecting sacrificial offerings. Where there's service, there's someone being served. The man who speaks to you of sacrifice, speaks of slaves and masters. And intends to be the master."
--Ayn Rand