After some discussions with RIM and IBM, the good people at IBM support, thanks to Steven Kyle who handled my PMR, were able to recreate the problem on a test server.
It seems the installation of BES 4.1.6 alters the notes.ini file
Lotus Notes Traveler has two components, a Server and an HTTP Servlet. The Server communicates with the users mail servers, stores history information etc and the HTTP Servlet communicates with the devices. When I installed the BES 4.1.6 Server it added this parameter to the notes.ini file which basically disables any Java based HTTP Servlet:
They removed this field from the notes.ini file and restarted the Domino Server and the Lotus Notes Traveler servlet started without problem and the device began syncing again. If the Lotus Notes Traveler Servlet starts successfully you will see a message similar to this on the Domino Console when the HTTP Server is starting:
HTTP JVM: com.lotus.sync.servlet.TravelerServlet: init
HTTP JVM: Traveler 18.104.22.168.200807181242: debug = false
So the questions for Blackberry and us in production are:
1) Why do they add HTTPDisableJVM=1 to the notes.ini file?
2) Will BES break if this parameter is removed?
Haven't tested it yet, harwdare failure this morning, but if it resolves it for you. Great.
PS - Don't forget IBM released a hotfix on the 24th for Lotus Traveler. Go get it, read the instructions first and then upgrade it.