For anyone that is running 6.4. It seems that in some instances an important index isn't being created on the w3t_Last table. If the index isn't created your forum will start to slow down. You can check to make sure this index has been created by running the following sql command:
SHOW KEYS FROM w3t_Last
This should return 2 results something like this:
Table Non_unique Key_name Seq_in_index Column_name Collation Cardinality Sub_part Packed Comment
w3t_Last 0 PRIMARY 1 L_Uid A
w3t_Last 0 PRIMARY 2 L_Board A 17259
If you don't see two PRIMARY keys, then this index didn't get created. In that case you will need to run the following 2 sql commands:
DELETE FROM w3t_Last
ALTER TABLE w3t_Last
ADD PRIMARY KEY Last_index(L_Uid,L_Board)
This will make it so all posts are unread for every user, but the index should be created at this point. You can verify this by running the SHOW KEYS FROM w3t_Last command up above and checking for the 2 returned results.
If you have a custom table prefix you will need to replace w3t_ with your prefix on all the commands.
For those that do need to create the index manually, if you can let me know that would be great so I can see how widespread of an issue this is.