Hi tmdar,
Were you able to see any changes upon changing the "samples per channel" parameter? You're right, it is possible that noise in the signal is being picked up as an event as well. Also, avoid running any unnecessary applcations on your computer while running this, or try running on a different machine to see if the results vary.
LabVIEW comes with a Filter Express VI (Express >> Analysis >> Filter) which you can experiment with to perform different types of filtering. However, since this filtering is performed after the data has been acquired, it may not help with the data acquisition issue. You may need an external filter. Before taking this step, you should verify if the problem is in fact signal noise. Since you're using one counter for "Low Frequency with 1 Counter", you can use the other counter to generate a pulse train, which you can feed as the input for your counting, to see if you can get up to a higher frequency. If this works, the problem is likely with the signal source. Otherwise, the issue would likely be the system or the code (please verify that you're using the shipping example, "Measure Dig Frequency - Low Freq 1 Ctr")
Thanks,
Lesley Y.