Hi Mahati,
I'd be a bit more interested in what your code looks like. The 6259 should have a DMA channel for each counter input task, so I'm not exactly sure why the error might be ocurring without seeing how you have everything configured.
In the meantime, the attached example should work around the problem (it doesn't used buffered counter inputs--are you sure you need to perform a buffered frequency measurement?). One caveat is that if you don't connect an input signal to either one of the counters the loop will timeout after 10 seconds (but this is true for buffered counter frequency measurements as well).
What are the frequencies you are trying to measure? Noise on your input signal could result in extra pulses being detected which would show up as a higher frequency. You can remove this with digital filtering using a DAQmx Channel Property Node (as explained in this post).
Aside from this, there will be some jitter to your measurements (noticeable at higher frequencies) since the frequency measurement is done by measuring the duration of the period of your signal and inverting. This jitter is ±1 tick of the counter's timebase.
I'd still like to see your code if possible, I am a bit curious about what might be going on in your situation.
Best Regards,
John Passiak
