you are correct. chrome does store flash cookies even when in incognito mode. i logged out of pandora in chrome, started up IE, noticed that i was logged out of pandora, then started up chrome in incognito mode, logged into panodra, then started up IE and noticed that i was now logged in to pandora.
Play this (addicting) game in Firefox - http://www.ferryhalim.com/orisinal/g3/bells.htm. It will record your high score. Open Chrome in incognito mode, die quickly, and see that it has kept your high score from Firefox.
Ok I'm back, after 'experimenting' with that flash game for the last 19 hours I can report that the music does get a bit annoying after hour 13 or so. Also Incognito mode doesn't stop the flash bugs.