Ashley - Got it! It's when using the webstorage facility - that's what's causing the problem. It also does it in the preview mode, but I hadn't cleared my appcache before, so that's why it seemed to be working.
I've put together a quick capx here: http://dl.dropbox.com/u/58315465/2012-02_BugTest1.capx
I hope this capx explains it. Basically, when the character gets through the exit hole it should restart the layout, but I think something in the webstorage is now stopping it creating the value. I now don't think it was the sub-event that was the problem in the first place, I just happen to have webstorage events in my sub-events.
...I think I've created the capx the right way to show what's going on... essentially this is a roughcut of what is happening in my main project
Let me know if you need anything else, Ashley. Look forward to hearing your take.