Hi Henry,
Installing BI4.0 SP07 - Then upgrading to BI4.1 completely broke the Server components. Whilst I was able to access BI Launchpad, I was unable to launch Web Intelligence from the My Applications sidebar, nor was I able to access any documents from the Documents tab, no error messages appeared, everything just hung.
I've gone back to my original VM now and I'm going to attempt a redeploy of the WAR files using the WDeploy tool. I'm at a loss to explain this, perhaps I need to further configure Windows Server 2012, so if WDeploy doesn't do anything, I'll try splitting the APS, etc
Otherwise, I'll need to create this as a new system on the SAP Support Portal and raise a support message using the special prefix you mentioned in an earlier post.
Ian