I am having the exact same issue with my WP 3.5.1 installation (GoDaddy hosted shared server; PHP 5.3). The entire website is no longer accessible and will not load after I make changes to the WYSIJA configuration. This happens on an intermittent basis not consistently.
I've reached out to Kim about this issue but perhaps you can assist as the exact same issue has already risen for another WYSIJA user. I can't access my website (even the admin dashboard) from any browser or any device.
The only workaround that I have found is to uninstall the plugin and wait a bit. I'd really like to get it working though as I think you guys have developed an optimal solution. Please advise how best to resolve. Thanks.