I just pulled some hair out over this problem. I discovered that stylish-select was causing problems when using jQuery and Prototype simultaneously (using jQuery's noConflict() method). This is due to two problems:
Firstly, this plugin uses the $ alias for the jQuery method, which may or may not refer to Prototype instead (I think it's conventional for plugins to use the full name?).
Secondly, this plugin adds to the Array prototype, which causes really major problems with Prototype for reasons beyond me (all event binding seems to stop working).
I hope this information is useful to somebody.