We have made many customizations to the CommerceManager app. I couldn't list the entire changes we have made since there are plenty and they touch almost every aspect of the application. Notice that we haven't changed the Business layer and Data layer and only extended them using classes that inherit from the core.
The customer have been playing around with the virtual page functionality recently and we are using it heavily on that specific website. So i think there is a good lead on that one.
The application used to work without a hitch since April last year and it only started throwing those excxceptions 2 weeks ago.
Thanks again for the help,
Aviad
Netcraft