Did you check the DVCS plugin version? Regarding the new Github API, JIRA must be using the latest version of the DVCS plugin to properly work with this repo.
For JIRA 4.4 - 4.4.5, you should use the version 0.15.11. For JIRA 5.0 to latest version, you should use 1.0.3.
Since you're using an AOD instance, I'd suggest to raise a support ticket for double check this info.
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