Steven, thanks for the support on this.
If it's any help here's more detail on my situation.
WP 3.6, using E2M 1.1.5 was working fine and still have one site running fine on this version, not upgraded to E2M 1.1.6 yet.
WP 3.6, upgrade to E2M hit problems during the upgrade process due to server timeout on one of my sites. So slowdown started during the installation of E2M 1.1.6.
Disabled E2M 1.1.6 and site (all pages in Admin and public side) was back to normal.
Uninstalled E2M 1.1.6 and uploaded E2M 1.1.1 plugin folder from a backup of the site. As soon as the plugin is installed the site slows again.
Uninstalled E2M 1.1.1 and uploaded 1.1.5 from backup and site slowed again.
Not sure if there's more to loading the plugin than just copying the E2M folder from a backup of the site? Bit confused how downgrading the plugin doesn't help when it was working fine with the older versions before. I verified the plugin folder and tables in the DB were removed after uninstalling each version. I verified the tables were created and populated with defaults after install.
The smallest site I have this issue on also has these plugins enabled:
"Contact Form 7", "Easy FancyBox", "Optimize Database after Deleting Revisions", "Show Menu Shortcode", "Soliloquy Lite", "WordPress SEO". It is using a child of Responsive theme from ThemeID, CyberChimps. There are minimal changes in the functions.php file as the site is still under development.
As soon as I can I will try disabling all other plugins and set the theme to a WP supplied one to see if it makes a difference.
Hope that will help.