I have been through the manual upgrade 3.6.1 to 3.6.4 and that seems to have gone ok. That got me to thinking - should I export the settings as a .txt file from the old 3.6.1 and then import them into the 3.6.4 as part of the process or is that likely to cause a problem.

all the settings are stored in the database, which you backup before doing major changes...right???
(good plugin -> wp-dbmanager)

The main reason for the export/import is for backup and for moving the settings to a new site

Many thanks for that - use xcloner to back up and seems to work well. I have a site set up just for testing stuff so tried the upgrade on that.