That's because Pro Tools has a 32 channel I/O limit. Pro Tools versions 9 and higher only see the first 32 inputs and the first 32 Outputs in the device driver. This was a design limitation put in by Avid for 3rd party interfaces. You'll need to use a different DAW like Studio One, Nuendo, Cubase, any DAW really as most do not have this limitation.
Contact Avid to make the request for them to change it, this not anything we can do to influence their software design.