Base functionality appears broken

So I've noted a few issues raised about this revolving around the autoload.php issue.

I've taken the submitted pull request and manually added the hardcoded paths as they match my current system and as a brief bodge to solve that issue but despite the scoring server offering a json format string including the team name, creating a link on each base challenge (it's a little ambiguous in the docs if one should specify protocol (e.g. http://) or just ip:port) and starting a game with active teams who share the names of the flags...

The challenges never get scored appropriately.

It's a bit late in the day here (koth competition is tomorrow) but is anyone able to offer some pointers. Other than following the modifications in the PR around languages, bases and scoring.php I'm running code freshly git pulled about 8 hours ago.