If attempting to bulk load preferences here are the locations of the files that contain the internal names for the string values. All of them are located from the Windchill/SRC folder.
We have been working on a similar issue as we are building a second servr to use with secure projects and wanted to transfer preference settings from our production server.
Currentlly we are using a combination of a report which extracts all preference instance settings for site and org level (ie any preferences changed from default) which we output as a TSV file. We then feed this into a vb app we have written which separates them into site level and org level load xml files. We can then read these directly into the new system via wt.load.loadFromFile.
The only issue we have at the moment is promotion preferences. These export from the production system OK, but when we import them to the new server they do not show up in the UI while all other new instances do, so we have to remove these before importing (or create the preferences first through the GUI.
All other prefernce instances transfer fine though.
Nice to see they have thought about this a bit more with WC10.