Instead of repeatly unconfigure the counter and reconfigure it again repeatly, you may want to just generate a continuous pulse train on one counter and use a second counter to gate it. The counter that is generating the pulse train will only output when the gate is high, so make sure that the gate is high for 5 pulses and low for 100 milliseconds. Another good thing about this approach is that you don't need to rely on windows timer to wait 100 milliseconds, instead a more deterministic and accurate 100 milliseconds calculated by the counter/timer's high accuracy oscillator. I have a feeling that the error message is coming from repeatly unconfigure and configure the counter in a loop.
