Tags Completely Broke

Been working on a new MU install for a little while.

Got to the stage where we had a nice new homepage and a bunch of plugins.

Then, the entire tags structure just broke, each resolving to a 404 error page - despite them showing fine on blog pages.

Now, were re-installing MU from scratch but just wanted to ask if anyone had experienced this before? We took apart all the plugins and mu-plugins and custom edits one-by-one without any luck. Checked all the paths and the server permissions but still no joy.

Were guessing some core changes mustve been made by something..