Help! Z axis not homing

I have a combo table Router/Plasma I have had for 7 years now. I finally decided to upgrade it with Homing/Limit switches. It has a seperae profile for Router and Plasma, I started with the router and got everything working, worked out all the bugs then copied my settings and went to the plasma profile and set everything up. I have everything working great on the Router profile but when I switch to the Plasma profile the Z axis will not do anything when I Ref All Home. I have been through all the cofig settings and ports n pins comparing the 2 and can not find anything different in the 2 profiles. I have been through all the issues I see posted about slaves directions and such and have worked out all the bugs except the z axis on the plasma. IS there something I am missing because of the plasma function in that profile? I have read countless post about homing and limit switches and have not seen this issue listed.