The thing about collations is that although the database has its own collation, every table, and every column can have its own collation. If not specified it takes the default of its parent object, but can be different.
When you change collation of the database, it will be the new default for all new tables and columns, but it doesn't change the collation of existing objects inside the database. You have to go and change manually the collation of every table and column.
Luckily there are scripts available on the internet that can do the job. I am not going to recommend any as I haven't tried them but here are few links:
http://www.codeproject.com/Articles/302405/The-Easy-way-of-changing-Collation-of-all-Database
Update Collation of all fields in database on the fly
http://www.sqlservercentral.com/Forums/Topic820675-146-1.aspx
If you need to have different collation on two objects or can't change collations - you can still JOIN between them using COLLATE command, and choosing the collation you want for join.
SELECT * FROM A JOIN B ON A.Text = B.Text COLLATE Latin1_General_CI_AS
or using default database collation:
SELECT * FROM A JOIN B ON A.Text = B.Text COLLATE DATABASE_DEFAULT