There's a bug in version 3.3.3 and it persists in version 3.3.5.
All the relations stored (in PMA database) for a database are deleted after drop any table of the same database.
It should delete all the relationships concerning the table that you are dropping but it make a delete for all relations stored for the database.
In the Mysql log:
DELETE FROM `phpmyadmin`.`pma_relation` WHERE master_db = 'exampledb'
If you are upgrading phpmyadmin from a prior version you should be carefully, because when you drop any table all you stored relations made before will go away.
I will attach the complete log for making easy to debug the problem.
Apache 2.2, PHP v5.2, Mysql 5.0