I’ve heard other people having a similar issue. There’s quite a bit of trouble shooting in that thread, but no resolution.
There were also some issues with the enclosure when the door was open on some firmware versions. I believe it’s been fixed in the latest firmware, but I’m not able to confirm that. Do you have the latest firmware? It looks like the latest version is 2.11.
Do you have an enclosure? If so, the door must be open during calibration. I’m not sure how to close the door and repeat the test. :-/
Can you verify that you mounted the Y axis correctly? It’s possible to put the screws in the wrong holes, which will shift the Y axis to the left. Although I think the offset is smaller, not 0.75".