Also strange is, when I plugin an external monitor, (non-mirrored config) it (sometimes) gets the default panel. However, it does not get the default Desktop folder. The default desktop should stay with the default pannel. 

Ideally the display to hold the default pannel/Desktop should be selectable from the Configure Display Settings applet.

Hmm.  AFAIK the panel currently does this:

1. Save the monitor number for each panel --- "this panel goes in monitor 0", or "monitor 1", etc.

2. If a monitor disappears, the corresponding panels get moved to another monitor (which one?  I'm not sure --- probably just monitor 0).

3. If a monitor appears again, the panels should move back to it.

So Magnus's problem is that (3) isn't happening.  Somewhere, the panel is (re)writing its configuration to say "the panel is in monitor 0", rather than leaving "monitor 1" in the configuration.

Simon's problem is that (3) happens sometimes.  So, sometimes his panel configuration says "panel is in monitor 1" --- sometimes it is preserved, sometimes it isn't.

I'll look for the place where the panel saves this configuration; it's probably just rewriting it at the wrong time.

However, the *real* solution for this would be for the panel to not use monitor numbers (which can come and go as you add/remove monitors --- in most cases you'll just have monitors 0 and even 1, though).  Instead, the panel should be able to remember explicit monitor configurations --- grep for "keying monitor configurations" in http://live.gnome.org/RandR1.2

I've fixed this upstream. Yay!