I suspected the gecko 540 was overheating, and losing steps. Mariss said in a post that the gecko 540 would simply shut down if it got overheated. I went ahead and put a dual fan setup (from a home theater) blowing over it, and that helped it stay cooler. I also noticed that a company in Australia is selling a similar fan for use with gecko's. The gecko still gets warm to the touch - but not blazing hot like it used to. This seemed to help the problem - or maybe it was my imagination....
And by the way, stepper motors do run very warmly - you can touch them, but you wouldn't want to linger there.
On top of losing steps, my Z axis began to chatter and not move at all - found (with Ahren's help) that was a bad DB9 connector on one the motors that allowed two of the pins to retract and lose contact.
I was still losing steps...so I rebuilt my z axis and rechecked to make sure there was no binding anywhere. I also suspected that electrical noise from my router cable was getting in the signal wires to the motors - nope, that wasn't it.
I tried a new parallel port card in my Dell 2.8 MGHZ computer - couldn't get the dang thing to work. Still don't know why.
So a couple of weeks ago, suspecting it was my computer not putting out enough signal in a reliable stream through the parallel port, I finally bit the bullet and ordered a SmoothStepper board from Warp9...
http://www.warp9td.com. The short story is that it works - no more lost steps, or DRO's showing motion while the axis stays stationary. The challenge is that the documentation that comes with the SmoothStepper is sketchy - you have to read a lot of posts to figure out what to do. If I had it to do over again I would suggest you buy the board from soigeneris dot com. They seem to have a good support setup, and the owner (?) Jeff Birt is active on the boards.
I put the SmoothStepper board in my control box - it attaches to the computer through a USB cable. The board connects through a special ribbon cable and gender changer to the parallel port on the gecko.
If you are interested in this approach suggest you read a lot of posts here:
http://www.machsupport.com/forum/ind...oard,65.0.html. Warp9 also has a forum, which you may find useful.
If you are unwilling to go the SmoothStepper route, I suggest you try another computer with strong output through the parallel port.
Good Luck.