The only thing that is definitively cached for MyISAM is an index.

The key_buffer_size variables sets up how large the MyISAM Key Cache will be.

There are two suggestions I can offer

SUGGESTION #1 : Use a Dedicated Key Cache for the Table

Did you know you could create a keycache dedicated to one or more MyISAM tables? Suppose you have a table called mydb.mytable and you want to load the entire mytable.MYI file into it. Here are the steps to set this up:

STEP 01) Get the physical size of the table's .MYI file

Run this query

SELECT index_length MYISize FROM information_schema.tables
WHERE table_schema='mydb' AND table_name='mytable';

Suppose the query returns 1234567890 for MYISize. That's 1.114978 GB = 1177.3757 MB. Round that up to 1280M (that 1.25 GB).

STEP 02) Create the Buffer with that size

SET GLOBAL mykeycache.key_buffer_size = 1280 * 1024 * 1024;

STEP 03) Associate the cache with the indexes for mydb.mytable

CACHE INDEX mydb.mytable INTO mykeycache;

STEP 04) Load the Index Pages from the .MYI into the Dedicated Cache

LOAD INDEX INTO CACHE mykeycache;

That's all. All indexes for mydb.mytable are now in that cache only. Running these commands also removes the same index entries from the general MyISAM keycache.

You could create a startup script for mysql to preload the indexes.

I have written about this subject is past posts

• Aug 28, 2012 : MySQL InnoDB Index in swap
• Jun 09, 2012 : Can we assign mysql Key_buffer_size value for particular table?
• Mar 20, 2012 : optimal table design mysql with primay key and varchar value
• Jan 26, 2012 : Less RAM than Index_length MyISAM
• Dec 30, 2011 : Is splitting a 'users' table for authentication purposes a good idea?

As a sidenote, I would like to suggestion something optional. You could speed up the access time of MyISAM data by changing the ROW_FORMAT of the MyISAM you want. For the same MyISAM table mydb.mytable, here is what you do:

ALTER TABLE mydb.mytable ROW_FORMAT=Fixed;

That's it. This a good and bad side to changing ROW_FORMAT to Fixed

• GOOD SIDE : Queries hitting mydb.mytable will run 20-30% faster without any additional enhancements
• BAD SIDE : This bloats all VARCHAR columns and treats them as CHAR. This will bloat indexes that have VARCHAR columns as well. This could increase table and index sizes 80-100%
• My Past Posts Where I Discussed This
  • May 10, 2011 : What is the performance impact of using CHAR vs VARCHAR on a fixed-size field?
  • Jan 03, 2012 : Optimized my.cnf for high-end and busy server
  • May 03, 2012 : Which is faster, InnoDB or MyISAM?

SUGGESTION #2 : Switch the table's Storage Engine to InnoDB

If you switch that table to InnoDB, you set up the InnoDB Buffer Pool in such a way that data and indexes that enter the Buffer Pool will linger a lot longer. This will simulate what your original question is asking: Partially invalidating a cache. That way, mysqldumps, full table scans, and queries like these will have roadblocks to cache stampedes. The options to tweak are innodb_old_blocks_pct and innodb_old_blocks_time.

According to the Configuration Options section of the MySQL Documentation for the InnoDB Buffer Pool:

Setting innodb_old_blocks_time greater than 0 prevents one-time table scans from flooding the new sublist with blocks used only for the scan. Rows in a block read in for a scan are accessed many times in rapid succession, but the block is unused after that. If innodb_old_blocks_time is set to a value greater than time to process the block, the block remains in the “old” sublist and ages to the tail of the list to be evicted quickly. This way, blocks used only for a one-time scan do not act to the detriment of heavily used blocks in the new sublist.

innodb_old_blocks_time can be set at runtime, so you can change it temporarily while performing operations such as table scans and dumps:

SET GLOBAL innodb_old_blocks_time = 1000;... perform queries that scan tables ...
SET GLOBAL innodb_old_blocks_time = 0;

This strategy does not apply if your intent is to “warm up” the buffer pool by filling it with a table's content. For example, benchmark tests often perform a table or index scan at server startup, because that data would normally be in the buffer pool after a period of normal use. In this case, leave innodb_old_blocks_time set to 0, at least until the warmup phase is complete.

The table cache does not store data, only MySQL table structs. The query cache cannot return old results because all the queries sing it are invalidated on write, and selects are blocked until that happens (actually causing some contention problems).

I will not discard a MySQL bug, as you are using a 9-year old unsupported version of the server, but you were too quick to discard cache issues/errrors on the other many layers of your application (client, server code, connector, your report code running on the wrong server, etc.).

To solve problems like this, you need to monitor queries sent and results returned at MySQL level and others, so you have enough information to identify the problem. I also recommend you to get familiar with the mysql command line client, as it is the best way to debug server issues.