I have been running into some problems starting the server first time after M12 installation.

1) Tomcat could not establish a secure endpoint on 9443
Adding the options -Djazz.connector.sslProtocol=SSL_TLS -Djazz.connector.algorithm=IbmX509 to catalina.bat solved this problem (yes i am using the IBM Java Runtime that comes with the installation package.
I have been checking the catalina.bat in my RTC3.0 installation, it does not need these options. What has changed ?

2) I still get some problems with log4j

log4j:WARN Please initialize the log4j system properly.
javax.servlet.ServletException: Plug-in "com.ibm.rdm.web.htmlgen.servlet" was
able to instantiate class "com.ibm.rdm.web.htmlgen.servlet.HtmlgenServlet".
at org.eclipse.equinox.http.registry.internal.ServletManager$ServletWr
per.initializeDelegate(ServletManager.java:198)
at org.eclipse.equinox.http.registry.internal.ServletManager$ServletWr
per.init(ServletManager.java:171)
at org.eclipse.equinox.http.servlet.internal.ServletRegistration.init(
rvletRegistration.java:64)
at org.eclipse.equinox.http.servlet.internal.ProxyServlet.registerServ
t(ProxyServlet.java:142)
at org.eclipse.equinox.http.servlet.internal.HttpServiceImpl.registerS
vlet(HttpServiceImpl.java:59)
at org.eclipse.equinox.http.registry.internal.HttpRegistryManager.regi
erServlet(HttpRegistryManager.java:223)
at org.eclipse.equinox.http.registry.internal.HttpRegistryManager.addS
vletContribution(HttpRegistryManager.java:114)
at org.eclipse.equinox.http.registry.internal.ServletManager.added(Ser
etManager.java:136)
at org.eclipse.equinox.http.registry.internal.ExtensionPointTracker.op
(ExtensionPointTracker.java:75)
at org.eclipse.equinox.http.registry.internal.ServletManager.start(Ser
etManager.java:62)
at org.eclipse.equinox.http.registry.internal.HttpRegistryManager.star
HttpRegistryManager.java:85)
at org.eclipse.equinox.http.registry.internal.HttpServiceTracker.addin
ervice(HttpServiceTracker.java:58)
at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(Servi
Tracker.java:896)
at org.osgi.util.tracker.AbstractTracked.trackAdding(AbstractTracked.j
a:261)
at org.osgi.util.tracker.AbstractTracked.trackInitial(AbstractTracked.
va:184)
at org.osgi.util.tracker.ServiceTracker.open(ServiceTracker.java:339)
at org.osgi.util.tracker.ServiceTracker.open(ServiceTracker.java:273)
at org.eclipse.equinox.http.registry.internal.HttpServiceTracker.open(
tpServiceTracker.java:42)
at org.eclipse.equinox.http.registry.internal.Activator.addingService(
tivator.java:59)
at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(Servi
Tracker.java:896)
at org.osgi.util.tracker.AbstractTracked.trackAdding(AbstractTracked.j
a:261)
at org.osgi.util.tracker.AbstractTracked.trackInitial(AbstractTracked.
va:184)
at org.osgi.util.tracker.ServiceTracker.open(ServiceTracker.java:339)
at org.osgi.util.tracker.ServiceTracker.open(ServiceTracker.java:273)
at org.eclipse.equinox.http.registry.internal.Activator.start(Activato
java:37)
at org.eclipse.osgi.framework.internal.core.BundleContextImpl$1.run(Bu
leContextImpl.java:783)
at java.security.AccessController.doPrivileged(AccessController.java:2
)
at org.eclipse.osgi.framework.internal.core.BundleContextImpl.startAct
ator(BundleContextImpl.java:774)
at org.eclipse.osgi.framework.internal.core.BundleContextImpl.start(Bu
leContextImpl.java:755)
at org.eclipse.osgi.framework.internal.core.BundleHost.startWorker(Bun
eHost.java:352)
at org.eclipse.osgi.framework.internal.core.AbstractBundle.resume(Abst
ctBundle.java:370)
at org.eclipse.osgi.framework.internal.core.Framework.resumeBundle(Fra
work.java:1068)
at org.eclipse.osgi.framework.internal.core.StartLevelManager.resumeBu
les(StartLevelManager.java:557)
at org.eclipse.osgi.framework.internal.core.StartLevelManager.incFWSL(
artLevelManager.java:464)
at org.eclipse.osgi.framework.internal.core.StartLevelManager.doSetSta
Level(StartLevelManager.java:248)
at org.eclipse.osgi.framework.internal.core.StartLevelManager.dispatch
ent(StartLevelManager.java:445)
at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(Even
anager.java:227)
at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(Ev
tManager.java:337)
log4j:WARN No appenders could be found for logger (net.jazz.ajax/AjaxFramework