Hi Michael,
We see behavior like this a lot when there are Github accounts with lots of repositories and lots of commits.
Github has an API rate limit that can easily be tripped by trying to pull the commit history (what Jira does when syncing a repo). Your account has 5,000 requests per hour (from all sources - not just Jira) before Github starts rejecting API calls. Using a curl command and the credentials for the user you're syncing with in Jira, you can see if the rate limit has been tripped. I've had luck in the past contacting GitHub through their contact form to ask for a temporarily higher limit while the first-time or full syncs for all the repos complete.
Hope this helps,
Daniel
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