I do not know why you would want to run 1280x1024 on AGA tho, XTREME screenmode is to much in WB at least I think so but I guess it's individual. What screenmode do you use for 1024x768? I use HighGFX but I mostly keep my Amiga at 800x600 to keep it snappy 
Still scratching my head with this thing. I find the config tool very confusing mainly because of the 3 different settings for resolutions. One, the Amigas screenmode prefs and then the two Indi settings, Amiga mode and VGA mode?
I can chance the amigas screenmode prefs in workbench fine and I normally run wb in 1024 x 768. This looks nice, but ive recently upgraded my monitor from 4:3 to 16.9 and I wouldn't mind trying the HD720 mode.
Unfortunately. When I try this I get a message from the amiga saying:
"Can't open screen. Is this monitor driver installed?"
Then nothing happens. Stays on 1024x768. Does the Amigas screenprefs mode override the indi config tool or is it the other way around.
I really don't know why changing screen modes has to be this difficult.
Cheers
