Input pins working in ptest but not linuxcnc

I have been fighting with my input pins and have replaced every component in my system and reinstalled the software.
If I use Ptest the inputs show up perfectly but in Axis only pins 11 and 13 work.

If you have any suggestions I would greatly appreciate them!

it is difficult to comment on the small amount of information given , it would be helpful to know
which version of linuxcnc live cd , own kernel build etc ? , and also what bob or controller you are connecting to , and to help further please attach your Hal and INI files as attachments , the more information we have as to your hardware the better the advice .

Hi cncbasher

Thank your for answering!

I downloaded and installed the ubuntu-10.04-linuxcnc3-i386.iso, I am not sure where to get the kernel but Linuxcnc is 2.5.0. I have an Ebay special Chinese optoisolated BOB but I am testing straight to the port to eliminate all other components.
Here are the files you requested, I feel the error is there but I am new to this, its my first machine and I have minimal Linux experience.

I think I have figured out my own problem, it appears that the home switch does not show up on the Axis display. I change my setup to Home + minimum on each axis and it reports to the display in axis.

if you have a link to the bob you are using we can check for you ,
also beware some BoBS also require an enable pin , this can be linked to amplifier enable .
and you may need to invert some pins for them to work .