Amber,
I guess you have an issue with MySQL. Appears there are a large quantity of records for retrieving and the query can not obtain them before the time configured for the execution of the sentence expires.
If you can connect to the database using an SQL Client (MySQL Workbench) execute some sql sentences and see what is happeninng ...
About the caching test, "misses" are the files which does not are in the cache and the system must retrieves it from the source (the physical location of the files).
Jorge.