Layouts certainly are one of swing's worst offenders, but in its marginal defense the more complex layout managers were meant to be used with GUI builder tools. The fact that I've personally hand-coded stuff in GridBagLayout and SpringLayout mostly speaks to my questionable sanity levels.
There are tools to build Swing GUIs? When I first encountered Swing I was expected to do everything from a command line with my trusty text editor. GUI Builders cost money and the bean counters treated my labor as a fixed cost whereas they actually had to write a check to buy tools. In their accounting world, how efficiently I worked did not matter because I was on salary.
On the point at hand, if the behavior in post #3 is correct then I say let's move the preferences from GLOBAL to user. The only downside I can see is making some entries obsolete and that is being discussed elsewhere. While I found the code that gets a preference for a named user, I'm not sure it works the way I fear.