This seems to be fixed now - for my repo at least.

The GitHub guy saying it was a "JavaScript display error" is incorrect though. I was pulling a repo and getting an old version.

EDIT: I'm not getting the javaScript display error, but I'm still missing my commit, so I guess these errors are unrelated :/

Did you file a support ticket for this? It sounds like an unrelated problem. We can investigate if you let us know what repo is causing the problem. Visit http://support.github.com or email support@github.com.

I posted the name of the repo to the thread, and someone else on the thread is confirming the same problem.

It turns out that GitHub didn't lose any of my commits. All future readers should ignore my comments on this.

This was my fault. GitHub was never messed up.

For what it's worth, I was pulling & pushing just fine while the error was displayed on my repositories, but other people reported commits lost or mangled. Maybe there was something more to the Javascript display error?