HD I/O Strange behavior
 

I'm in process of setting up an HD3 system with three HD I/O interfaces. I have a total of 5 AD cards, 4 DA cards and 2 AES cards. In I/O setup I can see all 40 analog inputs and all 32 analog outputs. They are all enabled. But when I go to record enable a track and select the input for it, I only have the choice of the first 32 analog inputs.
The interfaces are plugged in in the following order:

HD Core> HD I/O#1 (1x AD card)
HD Accel 1 > HD I/O#2 (2x AD card) >HD I/O#3 (2x AD cards)
HD Accel 2> no interface hooked up

I don't have a third long digilink cable so that's why I daisy chain two interfaces off one HD Accel card. But even so, I only set up 32 inputs on that cable and the first 8 inputs on HD I/O#3 work fine.

Any ideas as to why the second bank of inputs on HD I/O#3 can't be selected as source for recording even though it is visible to Pro Tools in I/O Setup dialog?

Re: HD I/O Strange behavior
 

Is it also visible correctly in Hardware Setup?

I would not set this up this way.

If it were me, I would go:

HD Core> HD I/O#2 (2x AD card) >HD I/O#3 (2x AD cards)
HD Accel 1 > HD I/O#1 (1x AD card)
HD Accel 2> no interface hooked up

The way you have it hooked up is a little weird. I can't promise you this will solve your problem, but I would start there.