Historically this problem would occur when the wrong firmware was installed. Serial wiring and serial firmware only use three drivers (X, Y & Z). It is my understanding that V1 is no longer shipping any sort of serial firmware or wiring harness, so if you made the purchase recently, this is unlike to be the problem. Still, you should take a look at the version on the display when you boot the control board. It should have a ‘D’ at the end meaning dual endstop firmware.
Another thing you can do to troubleshoot the problem is to swap X1 and X2 as well as Y1 and Y2 connections at the control board and re-run your test. If the problem stays with the same motor, then it is highly likely a wiring issue. If the problem moves to a different motor, then you have a firmware or possibly driver issue.