Steps to replicate:

• Create a test issue on a given project using JIRA Default Workflow
• Go to the Issue Navigator and perform a search on this project
• The issue will be retrieved
• Create a new event associated to the Issue Created template
• Make a copy of JIRA Default Workflow and on the "create Issue" transition, change the event from Issue Created to the Custom Event created on the previous step
• Create a new issue
• Go to the issue navigator and perform a search on this project
• The issue created right after the change of events will not be displayed
• Run a background reindex on the instance
• Perform a search on the project again
• The issue still won't be displayed
• Run a full reindex
• Perform a search on the issue navigator for this project. This time the issue will be displayed.

I believe the event only sets the notification scheme, and it is not associated with indexing at all, but in this case, it seems to be related to it.

As a workaround solution: Please add the "Re-Index Issue" in the post function of the workflow transition if you wish to use the custom event.
https://confluence.atlassian.com/display/JIRAKB/New+created+issue+is+not+showing+on+the+issue+navigator