The saga continues. The "backwards" X and Y connections turned out to be my teenage son who thought switching a couple of plugs was funny. Ha ha. Switched those back, and I can say definitely that the labels on the Sherline box (formerly Linux, now Windows and Mach3) match up just fine under Mach 3. Problem solved.
After playing with the system, I've discovered another hurdle that has to be jumped every time you cold boot the system. The system needs a kick in the head to get going. For example, I'll go into MDI and try giving it an X or Y command. Nothing. I then use the arrow keys to jog the system, click back in the MDI box, and voila, it responds. I'm guessing, but even though you see the long string of system settings at the top right of the screen, I'm not convinced everything takes at startup. I wrote a little program called "wakey wakey" to set things, cancel offsets, etc. and then just jog the steppers a bit to get their blood flowing.
One fairly big mystery remains: (Noticed most in MDI by the way.) I'll give it an x.1 just to give it a nudge for testing, and it'll go a full inch. I'll then go x0.1, even though it's not supposed to need the leading zero, and I might get .1 inch or I might get another inch. In fact, often times if I type in the exact same command, I get no response at all. (Yep, I'm trying to stay aware of o versus 0, etc.) However, if I change the value to say x0.2, off it goes. Always works if I change the value, but most often does not work if I repeat a command. I have the same issues with Y; for some strange reason it will ignore the decimal point for a while. However, after dinking around for a while, things seem to settle down and things react as I ask them to, although still not 100%. I am totally baffled by this. Again, all this is in MDI. Running a program seems more reliable, but even here I get some oddball stuff. For example, a program I ran last night had an x.3, which it did fine, but a couple steps later I'll give it an x-.3 and it shoots farther back than the x.3 starting position.
So, something, somewhere, is doing some random scaling or something...I just can't figure it out. Help?