I will log into the site and retract my post. After debugging, I found the problem...and it was really lame. I'm using the Types and Views Plugins...and have around 60 taxonomies with 400 children that I am using for the custom post types generated by types and views. About 20 of my pages were carrying the same slugs as the types taxonomies. It's funny, because there had been no problem with this for over 3 months and the all of sudden I got zapped and started removing plugins.
After doing a database optimization and removing your plugin...the site functioned ok again for a couple days, and then once again I strated crashing the mysql. So, not your plugins fault. I apologize.