Guys thanks so much for your input.
I checked the ini file and added HOME_IS_SHARED = yes
Then looked in Hal file and found the Y axis was configured for min and max+home being attached to the motion pins. Rather than both-home-y being attached
So I changed this to:
# ---setup home / limit switch signals---
net both-home-y => axis.1.home-sw-in
net both-home-y => axis.1.neg-lim-sw-in
net both-home-y => axis.1.pos-lim-sw-in
All working is well now,.,,PCW your suggestion was right on the money...
I guess this was all result of editing the hal files rather than using Pncconf to modify my machine set up. On the plus side I am learning lots more about hal and the MESA setup so it's all good.
This machine is close to cutting metal now....just a bit of shiming on the Z axis bearings first.
Cheers
Andy