Homing failure only on Y axis

What happened made sense to me. If a home switch is already enabled on power up, Linuxcnc will think its on the wrong side of the home switch location and move off it before continuing with the home sequence. But in your case, the condition never cleared.

Always trust Linuxcnc's homing if it does not work as expected, always check hardware first!

Thanks Rod
If I had seen your comment first it would have been spot on
Cheers
Barry