From your explanation, your connections seem to be OK and you're using the VI correctly. When using the default settings, you should connect your signal to the source of counter 0 (pin 37) and the negative side of your signal to a digital ground.
Is your signal truly a TTL signal? There are certain specifications (rise time, fall time, voltage level, etc..) which the signal must meet to be TTL. I have an E-Series DAQ device and I can run the same program with a slow digital signal and it works perfectly. So, the only thing I would suggest is to make sure that your signal is a digital/TTL signal. The document below goes over the definition of a TTL signal.
I hope this helps.
What Is the Definition of a TTL (Transistor-Transistor Logic) Compatible Signal?
http://digital.ni.com/public.nsf/websearch/ACB4BD7550C4374C86256BFB0067A4BD?OpenDocument
Regards,
Todd D.