I've logged a bug here: https://bugs.adobe.com/jira/browse/FP-243
In short, if you have an application composed of many SWFs, the 'scriptTimeLimit' setting on the main SWF has no effect -- it is overridden by the 'scriptTimeLimit' of any child SWFs. We're loading lots of child SWFs in our application, some of them third-party, so we have no way of setting the 'scriptTimeLimit' on our applicaiton. Has anyone run into this, and did you find any workarounds?