Flash Builder 4 uses the OS file association to determine the standalone player location.
So if you want to change the player being launched, just change the default program association for .SWF files (Right click a SWF, say open with, choose the flashplayer.exe or flashplayerdebugger.exe you need, make sure "Always open this type of files with this program" is checked and hit OK).
In the next version of Flash Builder, there's an easy preference setting to change the player being launched.
Thank you for your answer, but as I said, I already tried to change windows default program, and it didn't work. But I manage to do otherwise (By replacing and renaming the FlashPlayer.exe Flash Builder was using by the one I wanted to use).
But anyway, i'm looking forward for this feature in the next Flash Builder version !
Ah, that is because Flash Professional had a bug where it would re-associate SWF files to players in its sub-directory every time it launches.
P.S: You can try out the beta version of Flash Builder at labs.adobe.com