Algorithmically, it is doing what your colleague says. But, do you see what it is doing ???

It is generating 10,000 temp tables each containing 1 row after traversing 317 million rows through in the InnoDB internal index. Each temp table is a complete regeneration of the rowids in sernumbers_results_2009 table along with executing handler_read_prev commands internally to sort the data by an index scan from the back of the internal rowid index. Also, please remember you are dealing with InnoDB. Who knows what Multiversioning (via MVCC) is going on so that the INSERT is completed without interference and with rollback capabilities.

Is there any reason why this query wouldn't work for you ???

INSERT INTO sernumbers_results_2009
SELECT * FROM sernumbers_results
ORDER BY rowid DESC LIMIT 10000;

This will definitely generate one temp table.

Give it a Try !!!

I hate the checking permissions issue.

You may have to disable key checks before the DROP DATABASE

SET unique_checks = 0;
SET foreign_key_checks = 0;
SET GLOBAL innodb_stats_on_metadata = 0;
DROP DATABASE db_madeintouch;
SET GLOBAL innodb_stats_on_metadata = 1;
SET foreign_key_checks = 1;
SET unique_checks = 1;

UPDATE 2013-04-15 18:04 EDT

I just noticed you have innodb_file_per_table OFF. What gives ?

• You currently have all the InnoDB data and the corresponding index sitting in a single file.
• Any CREATE TABLE statement must make data dictionary updates and look for space (small but annoying in this instance)
• Internal Fragmentation of ibdata1
• Dropping a table means scanning the table and its indexes for availability to lock. With data and index pages possibly fragmented, this takes spindles, seek time, and latency.
• See Pictorial Representation of ibdata1 to see everything that goes into ibdata1

Recommendation : Remove all Data and Index Pages from ibdata1

This will give ibdata1 a breather to handle just data dictionary and MVCC management. In addition, ibdata1 will stay rather lean and mean and can be read more quickly.

You will need to perform the InnoDB Infrastructure Cleanup. I wrote out all the steps back on October 29, 2010 in StackOverflow.

UPDATE 2013-04-22 08:10 EDT

Three suggestions

SUGGESTION 1 : I just noticed something else. You are using an ancient version of MySQL (5.0.45). You should think about upgrading to MySQL 5.6.11 as it performs significantly faster that MySQL 5.5 and way faster than MySQL 5.0.

SUGGESTION 2 : You should also go ahead and implement the InnoDB Infrastructure Cleanup.

SUGGESTION 3 : You should also check the disk itself. If the data is sitting on a RAID10 set, one of the disks may have an issues. Check the disk controller's battery as well because it can slow down disk caching and affect read performance.