I am not the developer ... but having just lost a couple of nights sleep over it, I will offer my opinion :-)
if you have the ability, why don't you try switching themes to 2012 or 2011 as well as deactivating everything. I am suspecting that the issue my plugin was causing was that it wanted to dictate a format for tables (one of the shortcodes) So possibly your theme or any custom CSS you have is causing an issue?
I only found the issue after I did a completely new install of WP on a testing server. If you can, you might try there, adding features in order of importance to your site, checking if it is broken along the way. It might be the easiest way to isolate what is going on. Often plugins and/or themes make changes to your code or tables that they may not completely clean up after themselves even if you delete the plugin.
Let me know if there is anything else I may be able to help with!