Save is not really save in Preferences/Setup
I'm guessing I'm not the first person who has bumped into this one. I found that when I went into setup and changed my library path reference, pressed save, then pressed the view button to show the web site, the web site came up with the old settings. I had to press "save" at the project level to have those values actually written to disk.
I don't know how you guys should solve this, but at a minimum, I would suggest keeping a dirty flag on setup values and if someone presses view (preview I think), then prompt them to save before the preview.
Again, my 2 cents.