The cause of the problem may be that your web application uses tomcat6.exe instead of catalina.bat to start up.  From my observations it seems tomcat6.exe as opposed to catalina.bat uses environment variables only for the 1st run to copy CATALINA_HOME and CATALINA_BASE values to Windows Registry. Thereafter these parameters start to live on their own;) I had one instance of Tomcat for my Openbravo developer stack and the other for Alfresco. Tomcat6.exe used old values regardless of completly separate instalation of Alfresco dev stack.
You can edit these and other variables directly via Windows Registry editor, the path is:

HKLM/SOFTWARE/Apache Software Foundation/…..

or more conveniently you can use tomcat6w.exe GUI:

tomcat6w //ES//<serviceName> (eg. tomcat6w //ES//alfrescoTomcat)

calls a neat window where you can edit variables you need to run your web app properly.

there’s also //MS// parameter which will call a simple application monitoring given service:

tomcat6w //MS//<serviceName>

If you want to read more about running Tomcat as Windows service with tomcat6.exe go to an article from Apache Tomcat documentation.

Hope this helps someone:)