This applies to the Saffire Pro 40, 26, 24, 24DSP, 14 and Liquid Saffire 56
Pro Tools 9 and higher only allow for the use of a maximum of 32 simultaneous inputs/outputs. For this reason if your input/output count when using two FireWire Saffires exceeds 32, you will not be able to pass audio on the inputs/outputs with a count above 32. Despite this, these inputs/outputs will show up in Pro Tools' I/O Setup.
For more information on input/output limitations see the Avid website.