I have these odd :0.0 and :0.1 dual screen setup. If I start something with the launcher, it will always show up on :0.1, even if I clicked the launcher on a panel on :0.0. Interestingly the launcher properties window shows up on the correct screen. From the xfce menu, it works correctly. I'm also pretty sure that in 4.4 this worked just fine. One tiny gtk app I wrote myself also gets launched on the correct screen. But everything else (thunar, mousepad, Terminal,...) appears on the second screen instead of the first.
I'll probably do some work to debug this myself, as I assume you guys don't have this setup. But if there is something that obviously changed between 4.4 and 4.6, please let me know.
Created attachment 2003 Patch to fix DISPLAY in the environment before gdk_spawn_on_screen
The problem is very straight-forward: it seems that gdk_spawn_on_screen still has the bug that it doesn't fix the environment to contain the correct DISPLAY variable (which is necessary to launch on the correct screen). This time I'll really file a bug with gdk about this, but in the meanwhile please apply the attached patch.
Hmm, p0llux was so nice to report this for me already last year when I stumbled upon that issue (in libxfce4gui). Unfortunately the gtk guys don't seem to care: http://bugzilla.gnome.org/show_bug.cgi?id=497727
Ok, final spam: For reference look at bug 3667.
Thanks, patch comitted in revision 28932.