Hi Erik,
thanks for reporting that!
I had a look at the code and it is definitely a bug but just a bug in what is reported to PD. So MS Amanda does not really score z ions when NLs are considered, it only tells PD that it did ;)
So no worries, the scoring is correct, just the visualization in PD is wrong as we report something wrong. We will fix that asap, sorry for the inconvenience!
Best regards,
Viktoria