Thanks Marcus but managed to find the culprit. Service was set up to read nsq files in a folder rather than the one file we use. There was a backup copy of the pre-server change nsq stored in the same folder and NPrint servce was therefore reading the schedule from this file as well.
So moving the offending file seems to have done the trick and a test schedule ran correctly.
The only issue now is that even though all the old schedules were made inactive, nsq saved and then moved to archive, NPrint monitor still shows the old schedules and hasn't removed them (even after a service restart). I'm hoping the service will eventually clean up the old schedules over time.
1. Please be aware that no version of QlikView 12 is supported by NPrinting 16.x. Requirements for NPrinting 16.x.x.x versions only
2. To clean up the Monitor:
i. stop the NPrinting server service
ii. remove the NSQs and/or Folders from the QlikView NPrinting Files list
iii. rename or delete this file: C:\ProgramData\NPrinting\Monitor\Schedules.xml
iv. add your NSQs and/or Folders to the list
v. start the NPrinting server service
HTH - Daniel.