apologies, I got mislead with other things on my plate...
Right - I can see that The Tomcat Application Management Application starts the service C:\Bitnami\TOMCAT~1.56-\APACHE~1\bin\tomcat7.exe //RS//tomcatstackTomcat
What this is telling me, is that it does not execute the various BAT files related to Catalina, it is executing the exe directly.
For example - I have modified the setenv.bat file for a few java environment variables which are not being read by the system.
Does this mean the Tomcat Application Management Application is basically not suitable for my requriement and that I should use the startup.bat to execute tomcat?
My thinking (which now looks like I'm wrong) was that the Tomcat Application Management Application would execute the startup.bat file therefore executing all the necessary customizations in setenv.bat, catalina.bat etc.
Thanks for your help.