Ok, well as I do have PM installed I will have to guess as the desktop.war is modified by the PM install, but I would say you should try editing headerPlus.jsp (if it exists) to redirect the logoff action to a custom logoff.jsp page that you will have to write using the J2EE SDK. It is probably worth you installing BOE XI + PM on a test machine - just so you can see the code in that doLogout.jsp as it will show you what is needed to log off a session (even though that file is still currently missing the all important CMS logoff code, even in the latest CHF - but that another story 
)
Have a look at Infoview Logoff button is not logging off the session?
Thats about all I can suggest,
Good luck
Rod
rodallen 
(BOB member since 2006-02-10)