The DAQ M Series documentation suggests that any PFI channel can be routed to a counter/timer. However, when measuring a signal frequency with a counter/timer on my PCI6259, it seems that only PFI9 can be used as the signal source for both counter/timers. How come? The documentation hints that any PFI line could be selected as one would expect.
What API / method are you using to create your frequency task?
In LabVIEW, you can use the DAQmx Channel Property Node attribute Counter Input -> Frequency -> Input Terminal to select any valid input terminal for your task.