Dual X screens

I have dual monitors on an NVIDIA card, configured as two separate X screens rather than Twinview because I need to rotate one of them. That works fine after editing xorg.conf (never touch Sax2) but all applications always open on the first (primary) screen, even when started from the panel on the second screen. As the two X screen configuration doesn’t allow for moving windows between them, this makes the second screen all but useless.
How do I enable opening application windows on the second screen when started from there? This used to work fine in Ubuntu and SUSE 11.0/KDE 3.5 - I am now using Gnome.

Have you tried creating a new panel in the second screen with app launchers? This is what I did for xfce and works before,sorry just can’t test it now cause I gave my second monitor to someone.
The problem I had before was for firefox not letting me open two instances on both screens.

Tried that but makes no difference. Shouldn’t be needed anyway because the default for two X screens is that each application runs in the screen it’s started from. I suspect SAX2 has written something fishy into xorg.conf that prevents it from operating normally, but I haven’t found it yet.
You can’t make Firefox, or any other application for that matter, run in both screens simultaneously.

I don’t understand. Why can you not move the apps to your second screen? How can you move your mouse on the second screen then?

You don’t understand the difference between Twinview (one big desktop) and separate X screens. In the latter, no applications can be moved between screens but the mouse cursor does move. You have two panels and, usually, applications run on the scrteen they’re started from. My problem is that they only run on Screen 0 even if started from Screen 1, making Screen 1 a waste of space.
I can force an application to run in Screen 1 by explicitly setting the DISPLAY environment variable but that requires starting it from a terminal.

Thanks for mentioning XFCE. Installed it and it seems to solve many of the problems I had with Gnome: not only the one mentioned above but also that I don’t actually now need a panel on the second monitor as all the applications are available via the right-click menu. I can now also have different backgrounds on both monitors, something I missed with Gnome.
There’ll probably be other issues though, early days yet…

Well my infatuation with XFCE didn’t last too long - suddenly the panels disappeared, on next login I couldn’t run anything to bring them back, and then keyboard input failed… A quick google seemed to indicate that XFCE is rather buggy. So I’m back with Gnome and its annoyances when using dual monitors.
Some of these, to be fair, are NVIDIA’s fault. Hope they’ll soon make good on their promises to support RandR 1.2 so I won’t have to use Xinerama and no 3D acceleration. But Gnome doesn’t help, with its inability to have two desktop backgrounds, and its current inability to run applications anything other than :0.0 when using two X screens. In short, XFCE nice and capable but unstable, Gnome mature and stable but incapable, and KDE just an unholy mess…
Sigh, the joys of Linux!