[Darryl Ramm]

When you look in Pro Tools what exactly do you see for the IO paths? Screenshot time..

What exact modules do you have in each chassis? Your signature is a bit confusing. If you just one 16x16 module in one chassis why not add the 2x6 module to the same chassis? Why does it need to be in a separate chassis?

Only Pro Tools HD/Ultimate using a DigiLink interface can access more than 32 inputs and outputs. For any other systems Pro Tools only works with the first 32 IO. I suspect the issue here is what does ProTools thinks the first 32 inputs and outputs actually are. If you can you need to map all the IO in Mastero to be below the 32 IO limit. I'd just contact Apogee support of your questions are any deeper.