So there was a great likelyness that the "Voodoo"-file in Devs:Monitors/ on the HD and on the Emergency Disk were the same and that this caused the problem.
As I had backupped my System3.9:devs/ before I started to re-install OS 3.9, I could delete the "Voodoo"-file in System3.9:devs/Monitors/ and replace it with the one from the backup.
Then I rebooted - et voila - no Emergancy Disk required anymore!
I don't think the Voodoo file was the real problem here, but rather the Tooltypes of it's icon.
The thing is that the standard "SETTINGSFILE=SYS:Devs/Picasso96Settings" Tooltypes line will not work when booting from the Emergency Disk, since this will cause P96 to look for the Picasso96Settings file on the AmigaOS3.9 CD, where it obviously cannot find it.
I guess that you have changed this line in the past, so that P96 loads it settings directly from the E.Disk instead.
A more correct line in this situation would be "SETTINGSFILE=Devs:Picasso96Settings". This will cause P96 to first look on the CD for the file, and then check out the floppy.
