Gary, this is a link to a stepper machine running a 3D file. Might help some.

http://www.youtube.com/watch?v=bApuwkkXTb8

Brett

Hey Guys, type in Jerking Stepper in Youtube to see the problem!

Have you run the drive test to see if that looks ok?
Can you swap over drives to see if the problem follows the drive?
Also check your power supply voltage to make sure it is steady when running all three axis simultaineously.
Hood

Hood, done all your questions still no change? have to slow down to 2400mm/min to get rid of the pulsing.My old servo system
ran 5000.

I would certainly expect faster than that if it is 1:1, my Bridgeport has steppers with 2.5:1 reduction and I get 2500mm/min on all axis so would think you should be looking at atleast 5000mm/min as I doubt its any heavier. Not sure what size steppers you have as its hard to say from a pic but look like they are about 916oz/in. What drives are you using and what is the stepping on them?
Hood

I'd check the power supply out too , both volts and current wise when all axis are moving together.
no voltage drops on the cables etc .

Dave

Hood, the stepper motors are 2550 oz/in. and 201 drives.

Hood, the drivers are 203v at 1 tenth not 201's

Hi Garyh,
Here is an interesting thread that may or may not interest you.
http://www.machsupport.com/forum/index.php/topic,1724.0.html
RC

Geckos are good drives but these are big steppers, the bigger the stepper the slower you will be able to spin it, or at least thats been my findings.

Hood