Check the value of innodb_thread_concurrency.

For my system increasing the value from 8 to 32, per the guidelines in the MySql documentation, caused a discernible decrease in the number of threads concurrently reporting the "freeing items" state. Also, the obesrved average query time dropped by an order of magnitude.

While this made a large difference in overall server performance, it was not the "freeing items" silver bullet. My hardware ecosystem leads me to hypothesize that this state is mostly seen on systems with "slow" disks (2x10k disks raid 1), and is less prevalent on systems with faster storage (12x15k disks raid 10). So, a check of disk performance may also be warranted.

Good Luck!

Also:

It is worth noting that the default value of innodb_thread_concurrency is radically different depending on what 5.0 point release is being used.

The default value has changed several times: 8 before MySQL 5.0.8, 20 (infinite) from 5.0.8 through 5.0.18, 0 (infinite) from 5.0.19 to 5.0.20, and 8 (finite) from 5.0.21 on. -- source

This means that a seemingly innocuous upgrade from 5.0.20 to 5.0.21 changed the default from infinite to 8, and brought along with it the performance ramifications.

I think I have a plausible explanation you find very intriguing.

When you loaded the MyISAM table, only one index got loaded into the .MYI file in a lopsided manner.

Which index would that be ? THE PRIMARY KEY. Why ?

Indexes usually use BTREEs. They are designed to collect keys into a single BTREE node and balance the BTREE internally until the BTREE is full. On the insert into the full node, the full tree node is split and the keys inside are divided.

Most often a BTREE node will split is when you load the keys in order. For proof, look at the worst case BTREE --- the balanced binary tree.

I have several posts in the DBA STackExchange where I mention how a balanced binary only has node with one key. I also mention how a leaf pages must rebalance about 45% of the time when inserting a new key. Here are those posts:

• Aug 03, 2011 : When should I rebuild indexes?
• Jun 28, 2012 : Benefits of BTREE in MySQL
• Oct 26, 2012 : How badly does innodb fragment in the face of somewhat out-of-order insertions?
• Nov 26, 2012 : Does the Int type primary key insert order affect query performance in MySQL?
• Jun 04, 2013 : Why would increase in innodb_buffer_pool_size slow down MySQL?

My working theory is that random inserts into the table may actually make the .MYI smaller by prevent tree node splits as much as possible.

In order to make this happen, you will have to something quite unusual. Ready for this ?

ALTER TABLE generic_dummy_table_name ORDER BY datetime;

or

ALTER TABLE generic_dummy_table_name ORDER BY user,datetime;

That right, you can reorder the physical rows of the table. This may make the indexes a different size by inducing BTREE splits on another index.

Try reordering the table. Then, mysqldump it and reload it. You may find that the .MYI may get smaller or bigger. You cannot really predict it.

Next time, try reloading the MyISAM table with a very large bulk insert buffer.

Just run

SET GLOBAL bulk_insert_buffer_size = 1024 * 1024 * 1024;

then connect to mysql and reload the mysqldump.

GIVE IT A TRY !!!