I configured X to get multiple monotors on my laptop. It works nicely with KDE. But one day, I had to switch runlevel from 4 to 3 and back from 3 to 4, then when I booted with both monitors the desktops where reversed between the two screens. The wallpaper and widgets set on the LVDS jumped to the VGA-0 and those of the VGA-0 to the LVDS.
I think the matter is not very serious and it should simple to solve so as to restore the original configuration. But for now i don't know which files should I have to touch.

Should be a simple matter of examining the Xorg configuration to set the monitors up how you need them to be. This can be done either through xorg.conf or by using the System Settings panel (needs krandrtray running at startup though, and success isn't ensured in all cases)