Hey Scott,
- which method did you use? Using a square is not accurate enough, and a square of this size and at same time of sufficient precision would cost many hundreds of dollars/euros. The best method is the compare diagonals method. No measuring is needed, just a bar gauge to compare them.
- did you not only check for rectangularity (“squared”), but also for coplanarity (“not twisted”)?
In both cases if it is not accurately adjusted, the Y movement can block.
Generally the question on this issue is: Have you ensured that your machine is rectangular (“squared”) (bar gauge) and coplanar (“not twisted”) (fishing line method).
If you made sure both of these, and the issue persists, I recommend checking one by one the points in this support document: