Papercut can hide print jobs if it thinks the user is offline. This should show up in the the log on the front page. Should say something like "(Username) is offline. Job was hidden from print release until user is online" There is a config for this to change that support told me to change to the recommended value.
The config key is: print-job.offline-if-no-contact-seconds
The default value is : 90 Seconds
They said to change it to: 86400
Which is a day.
Then jobs should appear in the job queue as soon as you change it, no restart of papercut needed.