When a Service Desk Agent creates a new issue through Jira and changes the Reporter to a standard user, that user do not receive any notifications. We tested changing the Reporter to one of the other licensed Agents and all notifications that are enabled are working perfectly. I have already made sure that the User Default Preferences for "Notify users of their own changes" is turned on.
Notification helper indicates there is no issue and that the Reporter is receiving the notification but they are not. We've tested with multiple users and none are receiving any notifications with which they are a Reporter on.

So basically, we know the notifications are working as a licensed Agent will receive them if they are set as the Reporter, but if a non-licensed user is set as the Reporter they do not receive any.