I have a big production web-application (Glassfish 3.1 + MySQL 5.5). All tables are InnoDB. Once per several days application totally hangs.
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in this case you have to create several different database table with same column each other and do not inset more then 3000 row per table, in this case if you want to enter more data into table you have to create another dynamic table(generate table using code) and insert new data into this table and access data from that table. in your condition if more and more table will have to generate then you have to create new database.
i think this tip will help you to design your database more carefully and solve error.