I'm not sure what this was, but I came to the following conclusions as I was installing under JBoss 5.1.0:
1. Some patches don't want you to be root.
2. Most of the time you need to run as root, i.e. after you upgrade, if you are going to do all the default SMTP binding and such.
3. If you are upgrading, your admin password had better be the default for the .acp installs that happen during upgrade. I figured this out too late. I thought I had backups for my alf_data and mysql databases, but I made a few attempts to restart the "old" version with those and couldn't get it before I gave up and went with clean versions. Suggestions - change the admin password to the default before upgrading and then you may change it back again.
Sorry I can't be more specific, but I did not keep good notes.