IQAN design Measure terminated when disconnecting the input from a PCNT channel.

The Ethernet measure terminates 1 out of 5 times when I unplug a 60Hz signal from a PCNT channel on a MC43FS I am running IQANdesign 5.03.14.5040. I am aware this sounds like something in my hardware; however, two things make me question that.

1. The problem seems to have gotten worse as I add complexity to the function group that uses the input.
2. If I edit the function group to use a PCNT channel that is not connected to the problematic input, the problem goes away. This points to software because IF this was a hardware problem caused by the input disconnection somehow causing a hardware issue that gets into the hardware of the Ethernet signal THEN I would expect the same action to cause the same problem going into an identical input.

I have not been able to replicate the problem using a much slower input signal that I am generating in a slightly different way. However, the levels of the signal are the same.

I am suspicious that the high-speed bouncing causes the input to do something strange that the causes the firmware a problem possibly by exceeding the maximum input frequency.