Last week I managed to fry one of my pololus (y axis) by shorting it out with a screwdriver. I ordered a generic stepstick driver to replace it. After installing it today and adjusting the current I am having a strange issue. Prints are compressed along the y axis. I printed a circular part, and it came out as an oval, compressed along y. Do I need to adjust something? I thought about the jumpers on the sanguino that control mistrusting, but I'm not sure if that might be the issue of not.

Could it be that your new stepstick uses a different chip (e.g. DRV8825 instead of A4988) which use different jumper setting for microstepping? So e.g. if the new stepstip is DRV8825 and is set to 1/32 and the old ones are A4988 at 1/16 you would get the y-axis scaled to 50%. To remedy this, you can either change the jumpers underneath the stepstick to use the same stepping (if possible) or change the steps per unit for the y-axis in your firmware accordingly.

That is exactly the issue! The board came with A4988 chips, but the new one is a DRV8825. After reading some more last night, I realized I need to switch some of the jumpers to make it work. Thanks so much for the confirmation!