My application works on a .swf but not .exe?

My application works perfects when I open it in its .swf format, but some buttons don't work correctly when I open it in its .exe format. It doesn't work correctly in HTML as well.  This is the error that flash gives me when I publish: Warning: No libraries were linked as Runtime Shared Libraries (RSLs) because of your publish settings: Windows Projector  I have tried to merge code, but it only removes the error and does not solve the problem?

P.S: I am using graphics and sounds that are linked inside the library