I'm using Captivate 7 and have had countless problems with javascript, but anyways... I'll avoid ranting about that.
When you publish it as an swf are you loading it from the .htm file? I've noticed that JavaScript only "worked"(haha, if you could...ok, no ranting..) by loading it in the .htm file. When I loaded the swf directly locally or from a web server it wouldn't work.
There are three or four files in Captivate 7: swf, htm, css, and js file. When I put all of those on the web server, and load the .htm file JavaScript... uh, "worked'.. yeah