Not quite round prints

Have a Prusa Reprap with Gen6 electronics. Hadn't used it for a while so updated the firmware when getting it set up and recalibrated.

Printing round items and they aren't coming out quite round. There is an intentional little jog on the perimeter. To try to narrow down the problem I made a cylinder with a hollow middle in OpenSCAD and printed with 2 different compueters and host SW and it is still there so I'm assuming it is something with Marlin. The jog is on all layers and I can see the motor making the move.

One computer has Win 7, Repetier Host and Slic3r.
The other computer has Win XP with Pronterface and Skeinforge. (looking to retire that computer)

The print with Repetier has the nubs in the NE and SW on both in inner and outer edges. The print with Pronterface has the nubs at NW and SE on the inside perimeter and NE and SW on the outside perimeter.

Any suggestions on what to try or where to look?
Thanks

Hi,

I struggled with the same problem for a couple of weeks. In my experience it is either that the steps per mm is different for x and y, or (what's even more likely) that the shafts for the y axis are not exactly in a 90 degree angle to the x axis. (assuming you have the pruse i2)

Hope this will solve your problem.