This is related to my previous question (http://devnet.jetbrains.net/message/5475956).
I've tried embedding the script directly in the page, using <bs:linkScript> and also a raw <script> tag, but all have the same behavior.
I can work around it by using a <c:set> variable, but it's pretty horrible, and I have to escape all the quotes in the script.
This seems like a bug whereby the selected build runner page layout gets loaded via ajax, but any included scripts in the new page section don't get parsed. Is this intentional? Forcing a page refresh would probably work, but goes against the idea of loading the runner settings section via ajax. Is there any other, better, solution that I might be able to use?