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Consistent position errors after a long program could indicate a step timing
or polarity issue. Too low direction setup or hold times could cause a lost step
at reversals. Wrong step polarity can also cause this issue as stepping on the
trailing edge of the step pulse (rather then the expected leading edge) will
decrease the expected hold time.

It might be worth either inverting the step polarity or increasing the setup/hold times,
at least to see if it changes anything.

Some of the cheaper fixed bearing blocks are sold with non angular contact bearings, this is something to check.
Until you perform a backlash test, and yes this can manifest as repeatable, you can not rule out a mechanical issue.

Thanks Rod. I'll look into upgrading to 2.10.