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Sounds like maybe a damaged step/dir output.

It could also be marginal drive if you are using differential
wiring to a step motor drive. (its suggested to use
single ended drive with opto-isolated step/dir inputs
and differential drive with servo drives with line receiver inputs)

You can check the STEP/DIR outputs with a voltmeter.

 When the 7I96S is first powered up, the STEP/DIR pins will
be in one state and when LinuxCNC is launched (before starting
any motion), the states will be reversed. With no load, the outputs
should  equal the 5V supply  voltage in one state and near 0V in
the other state.
 

I've been looking into RIO for couple of days, reading forums and one question i can't find the answer for, may be it is obvious for all but me, what is the data protocol used in RIO over the spi? is it the same as Mesa LBP16 commands requiring hostmot2 or something else?

I'm sorry.
It seems it was my misunderstanding.

I've had a problem for a few runs where my X axis has been stalling while traveling to the right, and today it completely stopped working entirely. I've traced the problem all the way back to the mesa board.

By plugging in the X axis control lines in Y or Z's control ports on the board, it functions as expected. That means its not the wiring, the drivers, not the stepper itself, but something on the Mesa itself.

I've not changed anything in the INI besides some homing offsets for quite some time and it functioned perfectly for a around 6 months prior. There has been some temperature increases, but the mesa is in cased with 2 120mm fans facing it.

Has anyone seen or had this problem before? Is there a solution you can suggest?