I know this is a real old post. But I had the same problem and was searching for a solution and found this post.
I finally figured out what my problem was. So I thought I'd post my solution here.
I assumed the only real difference between Mach4Lathe and Mach4Mill was screensets used. That doesn't appear to be the case. I had copied a customized Mach4Lathe profile for a mill profile then changed the screenset to wx4.set. My new mill profile wouldn't recognize code G90.
However when I started from scratch and copied Mach4Mill for my new mill profile. It would now recognize G90 just fine.