New Mach3 settings but limit switches do not work, using a JK02 breakout board help!

Hi All
I have lost most of my settings for powering my cnc router which uses mach3. Now all works ok after re configuring but the limit switches do not work. I am using a JK02 breakout board and the inputs appear to be working because the diagnostics in mach3 show the correct activity when all the limit switches are activated. I have checked the settings in the "Ports and Pins" and they appear OK. Is there some other setting which could be incorrect? I have also checked the Estop settings and they appear to be working OK. Any suggestions?

Regards JimK