Shouldn't the installation tell me that the upgrade path is not supported? I have seen that before with SEPM. I do not get that warning when upgrading. In any event here is what I see in the scm-server-0.log file. I see an entry saying the server schema is higher than the db schema and the server will then exit.
2012-06-04 17:10:40.733 THREAD 1 SEVERE: ================== Server Environment ===================
2012-06-04 17:10:40.733 THREAD 1 SEVERE: os.name = Windows Server 2008 R2
2012-06-04 17:10:40.733 THREAD 1 SEVERE: os.version = 6.1
2012-06-04 17:10:40.733 THREAD 1 SEVERE: os.arch = x86
2012-06-04 17:10:40.733 THREAD 1 SEVERE: java.version = 1.6.0_31
2012-06-04 17:10:40.733 THREAD 1 SEVERE: java.vendor = Sun Microsystems Inc.
2012-06-04 17:10:40.733 THREAD 1 SEVERE: java.vm.name = Java HotSpot(TM) Server VM
2012-06-04 17:10:40.733 THREAD 1 SEVERE: java.vm.version = 20.6-b01
2012-06-04 17:10:40.733 THREAD 1 SEVERE: java.home = C:\Program Files (x86)\Symantec\Symantec Endpoint Protection Manager\jre
2012-06-04 17:10:40.733 THREAD 1 SEVERE: catalina.home = C:\Program Files (x86)\Symantec\Symantec Endpoint Protection Manager\tomcat
2012-06-04 17:10:40.733 THREAD 1 SEVERE: java.user = null
2012-06-04 17:10:40.733 THREAD 1 SEVERE: user.language = en
2012-06-04 17:10:40.733 THREAD 1 SEVERE: user.country = US
2012-06-04 17:10:40.733 THREAD 1 SEVERE: scm.server.version = 12.1.1101.401
2012-06-04 17:10:40.796 THREAD 1 INFO: Server startup
2012-06-04 17:10:45.280 THREAD 1 SEVERE: The server schema is higher than the database schema. The server will now exit. Run the upgrade wizard to synchronize the schemas.
2012-06-04 17:10:45.874 THREAD 1 SEVERE: in: com.sygate.scm.server.servlet.StartupServlet
com.sygate.scm.server.util.ScmServerError: The server schema is higher than the database schema. The server will now exit. Run the upgrade wizard to synchronize the schemas.
at com.sygate.scm.server.servlet.StartupServlet.verifySchemaVersion(StartupServlet.java:491)
at com.sygate.scm.server.servlet.StartupServlet.registerServer(StartupServlet.java:357)
at com.sygate.scm.server.servlet.StartupServlet.init(StartupServlet.java:137)
at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1206)
at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:1026)
at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4421)
at org.apache.catalina.core.StandardContext.start(StandardContext.java:4734)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:799)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:779)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:601)
at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:675)
at org.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:601)
at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:502)
at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1317)
at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:324)
at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:142)
at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1065)
at org.apache.catalina.core.StandardHost.start(StandardHost.java:840)
at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1057)
at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:463)
at org.apache.catalina.core.StandardService.start(StandardService.java:525)
at org.apache.catalina.core.StandardServer.start(StandardServer.java:754)
at org.apache.catalina.startup.Catalina.start(Catalina.java:595)
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.start(Bootstrap.java:289)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)