You're getting this code because the state of the line is already at the state you want to measure when the measurement begins. For instance, if you're trying to measure a high pulse width, the PFI line is already in the high state when the measurement begins.
If the signal you are measuring consists of multiple pulses, you might switch the application type in the diagram to "triggered pulse width measurement". Otherwise, you'll need to make sure the pulse has not started before the counter measurement has begun.
hope this helps.
gus....