It's possible that you are triggering Tomcat 7's ability to run multiple versions of a webapp, although I would hope that they log that feature more explicitly.
On the other hand, if you are defining multiple virtual hosts and each host points to the same tomcat webapps directory, getting multiple instances of the webapp would be exactly what was expected. The apps and hosts are not two entity pools. Each host contains its own set of apps (parent/child relationship).
So you really need to define a separate webapps directory for each virtualHost.
An IDE is no substitute for an Intelligent Developer.