If this problem still exists and you have a public-view of the website, send me the link and I'll see what I can find. I think the flash notice is only shown when the media specified can't be played natively by the browser being used, which is not common unless you are using strange media. I think you can also change which formats are supplied and the player type preferred in the jPlayer constructor, if I recall correctly. Again, I'm happy to have a look at your code and see if anything jumps out if you'd like.
Nick C
(jPlaylister author, jPlayer user for a while)