Actually this problem wasn't specific to ScrollPane but was to do with mousewheel events being intercepted by the browser and not reaching the swf.
I managed to solve this in the index.html file when embedding the swf by setting wmode = "window" (previously it had been "opaque") - the wmode property "Sets the Window Mode property of the SWF file for transparency, layering, positioning, and rendering in the browser" http://helpx.adobe.com/flash/kb/flash-object-embed-tag-attributes.html