I have just found out when you disable third party cookie in Chrome settings, the third party flash cookies will also be disabled. This applies when you are using Chrome’s native flash player, but the third party flash cookie will still be avaiable if you are using Adobe’s flash player in Chrome.
This gives you quite inconsistant behaviour if your application is using flash cookie (shared objects).
It took me quite a while to figure out, hopefully it can help for other people.