It is easy to switch back to 1.3.1 after you have installed 1.4.1
Simple go to /System/Library/Frameworks/JavaVM.framework/Versions/
In this directory there is a sym link called 'CurrentJDK' that point to the 1.4.1 directory. change this sym link to point to the 1.3.1 directory.
you will have to be logged in as root or use sudo in order to do this.
This doesn't allow JRun to work with 1.4.1 but is a fix for people who have installed 1.4.1 and don't know how to switch back to 1.3.1 as their default Java VM.