MySQL Query Cache – Type of Queue Used

This is likely an artifact of the MySQL Query Cache.

You execute the SQL query, MySQL caches its result and the next execution if fast. When you run the script to insert the data in tables referenced by your query, the result cache gets invalidated and the query must be executed "for real" the next time.

From the MySQL documentation linked above:

A query mix consisting almost entirely of a fixed set of SELECT statements is much more likely to benefit from enabling the cache than a mix in which frequent INSERT statements cause continual invalidation of results in the cache.

The table cache does not store data, only MySQL table structs. The query cache cannot return old results because all the queries sing it are invalidated on write, and selects are blocked until that happens (actually causing some contention problems).

I will not discard a MySQL bug, as you are using a 9-year old unsupported version of the server, but you were too quick to discard cache issues/errrors on the other many layers of your application (client, server code, connector, your report code running on the wrong server, etc.).

To solve problems like this, you need to monitor queries sent and results returned at MySQL level and others, so you have enough information to identify the problem. I also recommend you to get familiar with the mysql command line client, as it is the best way to debug server issues.