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.