Excessive MySQL throughput

My last post was closed without any replies so Im trying this again.. Moderators if there is a problem with what Im saying I would at least appreciate an email about why before you close this post too.

[moderator HandySolo urges calmness, peace and inner relaxation as we deal with antispam filters. Your patience will always be appreciated. Thank you.]

About a week after upgrading to the most recent version of wordpress (2.3.3) I have seen an extreme increase in the mysql throughput served (100x), during high traffic times the load on the machine increases dramatically and can take in excess of 20 seconds to load pages and often time out. I have several other blogs running the same version of wordpress and the same plugins, though they receive much less traffic, there has been no change in mysql throughput (not even slightly).

The upgrade was done by unzipping the newest version, moving over our content, plugins, settings, and theme, so no old wordpress files (or possibly tainted files) exist in the current install.

The number of apache requests have not significantly increased to coincide with the numbers that we are seeing, nor have the number of mysql queries. I have tried disabling all wordpress plugins one by one and all at once, with no change in the throughput. Currently there are only 4 plugins installed and activated, Akismet, WP-Digg style paginator, WP-FLV, and a comment analysis plugin I wrote myself.

Previously the site handled all usage, even the digg effect on occasion, without even blinking.

Apache 2.0.54
PHP 5.2.5 with XCACHE
MySQL 4.1.11

The blog has almost 6000 posts with almost 100,000 comments.

I have munin graphs that show the excessive increase that happened quite dramatically last monday, I can post urls for those graphs if nessecary. Previously my thread was closed which might have been because I posted those urls.