That can be a tough one. Let me start by referring you to this thread, then come on back.
1. Somewhat surprisingly, the much cheaper USB-6210 supports much higher sample rates for counter tasks. This is because of its much larger onboard FIFO -- 127 samples instead of 2 samples for the 6281.
2. The combo of a tiny little 2-sample FIFO *and* USB limits you even more than if you had a PCI or PCIe desktop 6281.
3. As discussed in the referenced thread, if the error arises as a result of "false edges" due to noisy transitions, a digital filter could help. But your mention of a 5 microsecond accumulation time makes me suspect that your real pulse rate is simply too high for your hardware to keep up.
What *is* the highest pulse rate you can expect to see? And what's the pulse width of the signals produced by the APD?
4. Other than brief experiments, I've never really used the 2 counter freq measurements. Does your mention of 5 microsec measurement time mean that you were trying to operate at a 200 kHz sample rate?
Unfortunately, it doesn't surprise me that 200 kHz would be more than your device can sustain due to the combo of USB and 2-sample FIFO.
Do you have access to any other data acq devices to use for this app? The best candidates would be devices with a bigger counter FIFO, such as the USB-621x or the 63xx (either USB or PCIe).
-Kevin P
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