Here's the source of considerable frustration. After reading about problems some people have had with their PC's I shelled out for a brand new unit, very standard boring parts, Intel motherboard, Intel cpu, I figured I'd keep it simple and avoid any issues with some of the more colorful motherboards out there have. Yeah that worked real well, the parallel port on this motherboard turned out to be a nightmare, 5 vdc on pin 13, one of the input pins I needed to use for the limit switches and as I found out tonight, it was giving the z axis stepper motor fits, it pretty much didn't work at all. So tonight I dumped in a 10 cent cheap china parallel port card and presto all the weird stuff vanished and whoa all 250 pounds of z axis is moving up/down quite nicely. My limit switches work now also.
Tech note, thats a 4 pin Mic plug out the back taking 5vdc and 12vdc to the enclosures. A bunch of stuff uses 5vdc, I'm running the big enclosure fans on the 12vdc feed.
http://www.coilbuilders.com/pics/mill4.jpg