Homing direction problem

With my Denford Micromill the end switches are at the furthest extent of travel. There are no zero switches, so the homing has to be done at the max point. For some reason, both X and Y axes regularly go off in the wrong direction so never reach these switches, and pressing the end switch does not stop the steppers, even though the switches are connected correctly. I say regularly, but I can't point to anything that's different when they do this. They seem to be wired correctly, because jogging sends them in the right direction. The Z axis homes itself fine. I attach the hal and ini files although it feels like a hardware issue.

Update: I did a bit of reading here (original approach, I know) and discovered that changing the homing speed to negative sometimes fixes things. So I did this, and now the Z and X axes go in the right direction. But the X doesn't recognise the stop switch, so I never get to Y. Normally the stop switch is connected to ground, except when it it is pressed. Do I need a pullup resistor to tell the the Bob that the switch has been pressed?

Further update.
The X stop switch still has no effect. But I have measured the voltage on that pin on the bob, and when the switch is pressed, the voltage goes from 0 to 9V. (This surprised me - I was expecting 5V).

I've tried swapping round the input pins (and stepconf), but whichever one the X switch is connected to, it has no effect on stopping the stepper then moving.

I am baffled

Does the hal pin parport.0.pin-12-in change when you activate the switch?

Yes, although i have not traced it as far as the pc, only to the Bob. Is there a way of seeing what the pc is getting?

Yes, when LinuxCNC is running select machine --> show hal configuration and
select parport.0.pin-12-in from the list of pins, then select the "Watch" tab

Alternatively, in a terminal window when LinuxCNC is running, type:

halmeter pin parport.0.pin-12-in

So I have used Hal meter which shows all three switches go from false to true when pressed but don’t cause the steppers to stop

They are attached to my original post

I dont see no limit switches. Just home switches and they are not shared in the ini. So to me it looks like you have no limit switches.