It seems that installing 2 tomcats as a service on 1 win box is not as easy as next,next next. Here is the procedure.
I installed the second tomcat using this command:
tomcat5.exe //IS//ApacheTomcat2 --DisplayName="Apache Tomcat 5 2" --Install="C:/Program Files/Apache Software Foundation/Tomcat 5.5 2/bin/tomcat5.exe" --Jvm=auto --StartMode=jvm --StopMode=jvm --StartClass=org.apache.catalina.startup.Bootstrap --StartParams=start --StopClass=org.apache.catalina.startup.Bootstrap --StopParams=stop
Because in this line we named the new tomcat service as ApacheTomcat2. We have to rename the tomcat5w.exe process to ApacheTomcat2w.exe, because we called it like this, when we start the service it looks for the ServiceNamew.exe. After renaming you run the new ApacheTomcat2w.exe and insert all the settings from your firstly installed tomcat.