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You probably need to install a persistent cookie handler. The default one keeps cookies in memory, so they don't persist application restart.
Thanks for pointing me in the right direction.
I found this which was quite useful http://stackoverflow.com/questions/12349266/how-do-i-persist-cookies-when-using-httpurlconnection
And this http://docs.oracle.com/javase/tutorial/networking/cookies/custom.html
I just adapted it to serialize/deserialize a map.