I can't figure out what's going on here, but maybe this info will be enough.
It appears that PHP is sometimes keeping a DB connection open after it exits.  This makes it so the tables can't be dropped until they are flushed (the files are locked)

From my debugging, my guess is that a second connection may be made to the DB and one of them is not released by php.  In process explorer, I saw that there were 2 connections to a table, but they had different cases - one connection called the database "Test" and the other "test".  This is my best guess as to the problem.

The automatic connection on query feature may be starting the second connection.  I see no way to detect if a connection exists already or i'd test this..?