Really odd issue with end stops not working during Home command only  

Really odd issue with end stops not working during Home command only

So my printer was working fine but after roughly 2 rolls of filament the Y axis smooth rods were getting some significant grooves in them. The bearings when installed were quite rough, even with grease. So I just purchased and installed Igus rods and bearings. But that is another matter entirely.

Anyways, when I reassembled the printer I started with a self test. It passed, everything was fine.

I started an XYZ calibration test and after it did the finding 4 bed points it went to home. Here is were it gets weird. Once it hit the end stops the steppers both just kept running.

I hit the stop button and tried the self test again. It passed. X axis went away, close, clicked end stop, away, close, away, close clicked end stop, screen said X okay. Same process for the Y axis. Then it tested bed for temp and said "ALL OK" and went to go home position.

Again, once it hit the end stops the steppers just kept trying to run until I hit the stop button. After that I moved the X and Y axis away from the end stops and they clicked so they are 100% making contact and they are working because it "passes" the self test.

I checked the cables, they are fine. I tried the button on top of the Rambo case to reset the board, that did not work either.

Does anybody have any ideas?