Can't reverse after homing

I am having a strange issue I have been running a CNC router with a dual motor axis for a while very happily and have just put in a second limit switch on the dual axis so it unracks itself on home in case it gets out of square, and have a really odd issue.Before I home the machine all the non-dual axes work fine (though it won't let me use the dual axis, which is annoying), once I home the machine on the last joint to home (1) it stops being able to move in one direction on all axes. If I try and move it in the other direction it doesn't move. 

I am attaching the previous version which uses a different config of limit switches, and seems to work fine - davemill-vfd.hal & davemill-vfd.ini
The new config is davemill-vfd-ind.hal & davemill-vfd-ind.hal

Does this make any sense to anyone?
   thanks