You do not provide information on the queries or tables being used, so this is speculation.
Changing the collation on the database does not change the collation on objects already created. So, you probably have a mix of collations in your queries. Such a mix can actually prevent the use of indexes, when they would otherwise be used.
To fix this, you would need to recreate all the objects in the database (including indexes) to use the new collation.
Here is another question about this topic.