It looks like I spoke too soon about everything being fine with the customised version of Jetspeed. After playing around with it for a bit it got slower and slower then fell over. All attempts to restart it failed. It seems that the 64MB JVM default wasn't enough. This led to a corruption of the database when it expired and a return to all the faults of the previous attempts: failure to login etc.
So I tried again with the 'minimal' install of Jetspeed, without any customisation. This reduces the heavy admin portlets to the minimum, but you have to modify the Jetspeed installation itself. They warn you not to do this, but the customised version already creates another application for Tomcat to struggle with. All I'll be altering are the layout and decorators, so I don't see the problem. I can also throw out alternative decorators since they won't be needed. I've got to run in a max of 64MB.
They reckon you only need '1 MB' for the basic Jetspeed, and '2 MB' for the customised builds, which I just don't believe. You can't even run a JVM that says 'hello world' in that much RAM, but it does show that you need less for Jetspeed in the raw.