Hi super-neuron,
If you look at the pinout map for the PCI-6259 in Measurement and Automation Explorer (MAX), below the pinout diagram, it mentions that the default pin for Counter 0 Output is PFI12 (pin 2). This is the reason why you will not see Ctr0Out in your list of terminals in LabVIEW.
I hope this helps,
S_Hong
National Instruments
Applications Engineer