It almost certainly has to do with the resolution change when using these programs (if you manually change the resolution of your KDE desktop to something considerably lower than native, it will probably need to shuffle icons around as well to avoid sending them off-screen). However, I don't know what you can do to prevent this from happening (I do not use KDE so I don't know if this is normal behaviour or if you can somehow lock icons to their place). Google led me
here which suggests some possible fixes (namely the second-last post) but it's not really ideal...
