XY motors are running at different speed in CoreXY

HI,
I am trying to rebuild my printer. it has corexy setup, running with nema 17 motors.
I uploaded the marlin firmware into custom build RAMPS board, it uploads successfully. When I press home X or home Y button in repetier host, axis' started going diagonally. After hitting the end-stops, both motors started continuous beeping sound. Both end-stops are working fine.
So for testing, I unplugged the XY motors and connect the wires with two another motors. I noticed that one motor is running fast or slow than the other. I checked all necessary setting for this in marlin, like homing speed, steps per mm, acceleration, micro-stepping, motor current, feedrate etc., but all are same for both motors.
Please help me out here.
Fun fact: Same code was working fine for another machine.

microstepping is set with jumpers on ramps for some stepper drivers. it is independent of firmware settings

I understand, but it is same for both drivers.

Check the jumpers again. They can look right and not be on right. They can also lose their metal contacts so all you have is a plastic shell.

Also if there is a bad solder joint on a stepper driver it can do the same thing.

"custom build RAMPS board"????

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Ultra MegaMax Dominator 3D printer: [drmrehorst.blogspot.com]

Reply to @Dust and @the_digital_dentist
the board is custom built TMC board using TMC2130 drivers. So no jumpers, all you have to do is set the microstepping in firmware.

Why didn't you mention you where using TMC2130 sooner?

What other essential information are you withholding?

could one of the steppers you grabbed be a 0.9 degree stepper?

I thought it wasn't necessary.
And no, both motors are 1.8 degree step angle.

as a test switch off corexy and try in Cartesian mode, and verify X and Y are behaving (or not)