If the Delta-Link is set to MADI 56/28/14 channel mode, which may be necessary to interface witn some other equipment or to use varispeed, each MADI port can only transmit and receive 56 channels at 44.1 or 48 kHz, 28 channels at 88.2 or 96 kHz, or 14 channels at 176.4 or 192 kHz.
So for instance, at 96 kHz, channels 28-32 on MADI port A and channels 61 to 64 on MADI port B are not used.
The problem in this case is that the Setup I/O configuration in Pro Tools may still contain paths that use these channels.
If the Delta-Link is set to 56/28/14 channel mode, you should ensure that Pro Tools tracks are not assigned to unavailable inputs/outputs.
Preferably, you should edit the Pro Tools Setup I/O, deleting paths that use unavailable inputs and outputs.