Hi,
The first thing you should check whenever this behavior comes up is the signal you are inputing in the FP-CTR module. This module has a threshold in the range of 6 to 10 V, that means the threshold of a particular module might be 10 V, so in order to garantee proper behavior your input signal should be at least at the level of 10 V.
Monitor the signal in the input, because the LEDs have a slightly lower threshold then the input itself, so your signal might be activating the LED and not activating the input. The fact that you have to power cycle the module might somehow make your signal level to come back to the expected level.
So the key point in this case is to monitor the input signal is in the necessary range.
Best Regards
Andre Oliveira
Applications Engineer
National Instruments