Hi yehya,
It is quite likely that what you are observing is noise. The DAQ-STC chip is capable of detecting signals as narrow as 10ns. This means that you could potentially have noise which is causing a misreading on the line. Unfortunately, the DAQ-STC hardware doesn't have immunity to noise of this type. It is up to the user to shield and minimize the noise to the counter inputs.
The PCI-6601 boards on the other hand of built-in filtering which allows the programmer to specify the minimum pulse width that will be applied to the counter inputs. This way, it minimizes the effects of noise.
The following knowledge base discusses how to create this type of filter using the DAQ-STC but it requires a counter to be used as a filter for only one sign
al. Not sure how useful that will be in your case. Typically, it will help to twist a ground signal around your counter signal. This acts as shield to minimize the effects of noise.
Anyway, hope that helps. Have a good day.
Ron