I'd suggest checking if the installed version of GreenHopper is compatible with JIRA. As you JIRA is 5.2.1 GreenHopper should be in version 6.1.0. If you still face issues, please try restarting your JIRA and then apply a reindex on it.
Let us know how it goes.
I'm using the latest JIRA with the latest Greenhopper (JIRA v5.2.1, Greenhopper v6.0.8).
I can see the Agile menu and if I open a project I can see some boards (Classic Task Board, Classic Chart Board, Classic Released Board).
My problem is that I can't see the Rapid boards that I was using before the JIRA upgrade and not sure where to look for them.
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