Yes, I am deploying from an active github repository. Commands like git status, git pull all work fine.
It might be something to do with the fact that when I first signed up with Hoptoad I was hosted on Codaset but now we're back at Github. origin master now equals a Github repo when at first install/run it was a pointing at codaset.
If you're not using capistrano for deployment, you'll need to provide the REVISION and REPO env variables to the rake task as well to take advantage of the Github integration; see lib/hoptoad_notifier/capistrano.rb for an example: