Hello Stephan,
In general, counter operations are performed in hardware on the counter chip, that means that something that happens in the operating system does not have influence on the way the counter works istelf.
But it may have influence on the VI that is reading the counter register. Depending on the way you program, if windows is just occupied with some other job to do, the vi may fail to read the counter register at the desired time, thus missing a sample - at the same time the counter register is not reset to zero and the next reading will be a higher count as you normally would expect.
You can prevent effects like this by using buffering. Its just the same procedure as for analog input - buffering prevents that you are losing samples. Have a look at examples like "count buffered edges" and I am sure you will see better results.
Ingo Schumacher
Systems Engineering Manager CEERNational Instruments Germany