Z Steppers Rough

[hazydaze]

I have an old home built Prusa I3V style printer. I found myself an extras SKR pro 1.2 and TFT35 I decided to use to upgrade my printer with. I also used the chance to upgrade to Marlin 2.1.2.1 and to put in some 2208 drivers to make it more quiet. I also decided to upgrade the extruder, hotend and part cooling fans.
Everything went fine and I've printed a few things but the hotend wasn't the upgrade I thought it would be and kept getting jammed so I modified and printed parts some to make my old hotend work with the new system.
I went through the firmware and set my probe offsets then ran the probe wizard to find my z offset. While doing that I noticed firmware was still using the old offsets so I reset EEPROM. This loaded the new offsets but when I reran the z probe wizard now my z steppers are rough like it's a loose connection.

The z motors are rough no matter if I home, auto-level, or manually move from the tft touch mode. However if I put it in marlin mode and jog z axis manually the motors run smooth and normal.
I can plug the z motors into x or y and they run smooth and normal and I can plug x and y motors into z and they run rough. Obviously I reset something in EEPROM it didn't like so I went through and reset feedrates and accel settings back to default or lower and I'm still having issues and just can't find what changed or what's causing the issue.