A couple of things:
You don't have to shut everything down, just close the cover -- I have a TiBook and I go all over with it. Usually I have CFMX running under both JRun and Tomcat -- sometimes, even the port.-- I very seldom stop ColdFusion, except to recycle some services for new database drivers, etc.
I assume you mean the debugging settings in the CFMX Administrator -- I have no problems retaining the settings across reboots of the system.
You have installed JRun in a non-standard location,
/opt/JRun4/ -- the standard (default ) location is
/Applications/JRun4/ -- this may be causing your permissions problems.
You should not run JRun ar CFMX as root user (
su root or
You are getting a database error -- What RDBMS are you using: At work? At home?
Is the database on the PowerBook or another machine?
Finally, if you think you have found a legitimate bug, you might want to contact Macromedia!