All you have to do is set the default website (or any website besides the Symantec Web Server) to use a non-standard port, then change the port on the conf.properties to use that website's port.
2009-11-01 13:11:58.203 SEVERE: ================== Server Environment ===================
2009-11-01 13:11:58.203 SEVERE: os.name = Windows 2003
2009-11-01 13:11:58.203 SEVERE: os.version = 5.2
2009-11-01 13:11:58.203 SEVERE: os.arch = x86
2009-11-01 13:11:58.203 SEVERE: java.version = 1.6.0_14
2009-11-01 13:11:58.203 SEVERE: java.vendor = Sun Microsystems Inc.
2009-11-01 13:11:58.203 SEVERE: java.vm.name = Java HotSpot(TM) Server VM
2009-11-01 13:11:58.203 SEVERE: java.vm.version = 14.0-b16
2009-11-01 13:11:58.203 SEVERE: java.home = C:\Program Files\Symantec\Symantec Endpoint Protection Manager\jdk\jre
2009-11-01 13:11:58.203 SEVERE: catalina.home = C:\Program Files\Symantec\Symantec Endpoint Protection Manager\tomcat
2009-11-01 13:11:58.203 SEVERE: java.user = null
2009-11-01 13:11:58.203 SEVERE: user.language = en
2009-11-01 13:11:58.203 SEVERE: user.country = US
2009-11-01 13:11:58.203 SEVERE: scm.server.version = 11.0.5002.333
2009-11-01 13:12:00.437 SEVERE: ================== StartClientTransport ===================
2009-11-01 13:12:00.468 SEVERE: Unknown Exception in: com.sygate.scm.server.servlet.StartupServlet
java.lang.Exception: HTTP 404 Not Found, URL:
http://localhost:8012/secars/secars.dll?action=34
at com.sygate.scm.common.communicate.Communicator.getRequestInputStream(Communicator.java:626)
at com.sygate.scm.server.util.ClientTransportHelper.startClientTransport(ClientTransportHelper.java:147)
at com.sygate.scm.server.servlet.StartupServlet.init(StartupServlet.java:106)
at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:880)
at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:768)
at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:3484)
at org.apache.catalina.core.StandardContext.start(StandardContext.java:3710)
at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1148)
at org.apache.catalina.core.StandardHost.start(StandardHost.java:697)
at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1148)
at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:311)
at org.apache.catalina.core.StandardService.start(StandardService.java:450)
at org.apache.catalina.core.StandardServer.start(StandardServer.java:2213)
at org.apache.catalina.startup.Catalina.start(Catalina.java:484)
at org.apache.catalina.startup.Catalina.execute(Catalina.java:371)
at org.apache.catalina.startup.Catalina.process(Catalina.java:134)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:151)
com.sygate.scm.common.communicate.CommunicationException: Unexpected server error. ErrorCode: 0x10010000
at com.sygate.scm.common.communicate.Communicator.getRequestInputStream(Communicator.java:650)
at com.sygate.scm.server.util.ClientTransportHelper.startClientTransport(ClientTransportHelper.java:147)
at com.sygate.scm.server.servlet.StartupServlet.init(StartupServlet.java:106)
at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:880)
at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:768)
at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:3484)
at org.apache.catalina.core.StandardContext.start(StandardContext.java:3710)
at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1148)
at org.apache.catalina.core.StandardHost.start(StandardHost.java:697)
at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1148)
at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:311)
at org.apache.catalina.core.StandardService.start(StandardService.java:450)
at org.apache.catalina.core.StandardServer.start(StandardServer.java:2213)
at org.apache.catalina.startup.Catalina.start(Catalina.java:484)
at org.apache.catalina.startup.Catalina.execute(Catalina.java:371)
at org.apache.catalina.startup.Catalina.process(Catalina.java:134)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:151)