AS3 Features not working outside of Flash Publish

I am having a strange issue where some AS3 features work when I publish directly from Flash by using Ctrl+Enter, but then if I launch the .swf directly from the folder where I publish it, things don’t work. For example, I have a movieclip set to buttonMode that launches a .pdf. This works when I use Ctrl+Enter, but when I launch from the folder it doesn’t even recognize that the MC is a button? Any ideas?
Thanks, Amanda