Published .swf Files ignore my AS Code

I've been working on s project for a week or so, testing it with Ctrl+Enter in Flash and I got it working just fine.  Tonight, for the first time, I tested it by just running the .swf file and none of the ActionScript works...primarily, the stop() command on the first frame, it just blows through my whole movie as if there's not a lick of code there.
I went back in Flash and tested it there with Ctrl+Enter and voilla...no problem.
Odd...
So I opened a brand new Flash file.  A plain document.  I put a keyframe on 40, then put a keyframe on 30 and put some plain text on the stage "this is some text"
I tested the movie, with Ctrl+Enter and, as expected, for awhile I saw nothing then "this is some text" appeared, then the movie got to the end and restarted.
So far so good.
I put a "stop()" in the first keyframe of the movie.  Ctrl+Enter to test it.  Nothing happened.  The movie was stopped.
Cool, so I published the .swf file.  When running the .swf the "this is some text" text did appear and the movie played as normal, COMPLETELY IGNORING MY CODE.
WFT?  I've checked my publish settings, I am publishing AS 3.0 and this is CS4 that I'm using.  Any help?

Hi kglad. The issue is more in AIR. When testing the .fla file in Flash Professional (CTRL + Enter), the file works as expected. However, if I publish the file using default settings in AIR, the stage just immediately begins flickering. I've upload the file to the following location.
http://www.sendspace.com/file/ki0pwk
Many thanks for the help.

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