Problem with Mesa Channel

I have a MESA 7i76e and think i have a problem with 2 of my step and direction channels, I cant get them to do anything.

I wired
Chanel 0 to Z
Chanel 1 to Y
Chanel 2 to X

and i spent a couple of days scratching my head as to why i couldn't get my x axis to move, I checked the wiring over and over re did it a couple of times, then i swapped x and y and X worked. I then found I couldn't get channel 3 to do anything either, channel 4 does work. So I have got my current machine working but I have plans for a rotary axis as well so could do with working out if i have something wrong config wise or if there is a problem with the board.

I have used Pnconf and have attached the view, I'm not good at the config of the mesa card yet, is there a way i can manually set pins to check the outputs?

Also the yellow Init light comes on when i use LinuxCNC which the manual said should be off.

Any help would be appreciated.
Thanks
Tim

I would expect odd behaviour from pncconf if multiple X axis are enabled

Also I dont think its an issue with pncconf but you have rather non-standard axis /stepgen mapping
more normal would be

X = 0
Y = 1
Z = 2

Can you try this mapping and disable the unused stepgens?

If this does not work, please post your hal and ini files here

The init light issue is probably firmware/ LinuxCNC version related
I dont think its significant

I'm aware my wiring is backwards to normal silly reason i wanted the order to match the encoders but that BOB is mounted the other way round. I can swap the X and Z cable no problem and see if that changes things.

I have tried it with only 1 X channel that's where i started but I will make a new config fresh from PNCconf without my MPG or any other mods and
X = 0
Y = 1
Z = 2
As i don't think I actual did that and post the config if its still an issue.

It wont be this eve as i'm on baby duty.
Thank-you for the prompt reply.
Tim