I'm having a similar issue. I installed the Seafile straight off the bat with MySQL, and I can login once using the admin password, but not again. If I am logged in, and try to reset my password it says my old password is incorrect.
I can drop the tables and re-setup Seafile and I can once again login, but only once. I have checked the EmailUsers table in the ccnet-db and find that before I login there is an MD5 encrypted password, but after I login it changes to something else with a pbkdf2sha256$10000$ string prefixed to it. I've hunted around the net for a potential answer but can't seem to find one. I am running MySQL 5.5 on Centos 6.5 if that helps any :-)
I have resorted to using SQLite which seems to work fine, but really would like to have a MySQL setup so that I don't have to stop Seafile in order to backup the data.