Doing sanity-checking for JIRA 6.1, I did the following steps:

1) Did a clean install of production-mode JIRA 6.1-RC1 BTF on Windows.
2) Followed the JIRA setup process.
3) Clicked Create Project from the dashboard gadget.
4) Selected a JIRA Agile project and followed the prompts to install JIRA Agile.
5) Entered my MAC credentials when instructed.

The installation appear to complete successfully, but when it redirected me back to the Create project dialog, the JIRA Agile project types were missing. Refreshing the page and restarting JIRA Agile did not bring them back.

On closer inspection by pobara and jderaedt, it became apparent that JIRA Agile was installed and running but not licensed. Version 6.3.0.2 had been installed. There were no errors in the logs. The license when pasted in manually works.