Just getting back to this thread and after a re-read, I think this is a hardware limitation.
Device specs for the USB-6341 declare a 25 MHz limit for what they refer to as an "external base clock." What this essentially *means* is that external signals faster than 25 MHz aren't guaranteed to get through the front-end interface circuitry to be counted. The internal counter itself *can* count at 100 MHz when it counts its own 100 MHz internal base clock.
Back in the day I used the PCI-6602 quite a bit. By comparison, it has specs for "maximum source frequency" (which I presume to mean external OR internal) of 80 MHz. Unfortunately its PCIe replacement, the 6612, is back to spec'ing the max frequency for edge counting at 25 MHz.
Offhand I don't know of a good workaround, unless bursts of >25 MHz pulses are rare enough that you can simply accept the measurement error of missing them. Otherwise you'll need a DAQ device that's capable of receiving 50 MHz pulses.
NI has a lot of DAQ devices I don't know much about so you can see what they would recommend. I'm sure there are 3rd party devices that have the specs, but those don't always integrate particularly well. The one thing I would know to try is a PCI-6602 (but you'd need to find a desktop PC that still supports PCI).
-Kevin P
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