Are you compiling the project into an .AIR file?
Publish/Build the .air file after you are done building in whichever program you are using, then run the .air application. Your app should work (nearly) identically as the ADL driven testing app.
I'm using Flash CS4 and exporting the .exe and other AIR components.
I am hoping to be able to test the .exe without having to install it.
Or do you have to install it in order to run it? Seems like an unnecesary pain-in-the-@ss if you have to install it every time to test it.
Adobe AIR applications are designed to be installed to run. Other than installing an application, the only way to test it out is to debug it in the authoring tool (i.e. Test Movie in Flash CS4).
However, almost everything that you can do in AIR can be tested from the authoring tool. There are a few things that can't -- offhand the ones I remember are testing application updates and launching an app at startup.
What is it that you're trying to test, that you can only test from the .exe rather than from Flash Professional?