HI,
Seems weird. I just did a test with an mp3 and it sounds the same. You can try loading in an uncompressed audio file like a .wav and see if that sounds better.
Or, I'm not sure if it will help. But you could try opening the Library (window>Library) and then finding your audio file in the Library. You can Right-click on it, and select "Properties" and try unchecking "use imported quality" and select "Raw" and click test to see if that sounds better. You can also try unclicking "Convert Stereo to Mono".
If you are using a native Flash (non-HTML5 canvas file) I am pretty sure that it exports the file to an SWF, and then converts the SWF to video, so this might help. If you are using a canvas file, I am not sure if the export is the same or not.
Give it a go. Hope it helps.
mark