I failed migrating the portal and had to create it from scratch. Almost 1 year later, i found out what caused the problem. Here it is. To be fair, it's a MySQL issue, not Liferay
The MySql database, since it got ported from a windows server to a Linux one, was exported with table names in Uppercase. When Liferay tries to connect to the database, it will not find the Liferay Model's tables, and will create new ones. Practically Liferay treats the Database as an empty one, and it starts as a fresh portal. I only found that, while exploring the database sometime later, and found out I had each Liferay Table both in uppercase and lowercase.
More info and solutions can be found here