The current Indivision AGA does not make the Amiga create new screen modes that it could not do by itself, it allows the screen modes that would normally be non-viewable by most monitors converted to screen modes that are viewable.
If you are having problems with the A4000 AGA version with some of the screen modes, there is a mod that can be done.
It's a 1K resistor between +5V and the CCK line which raises the peak to peak amplitude of the clock signal to over 4 Volts, Without it the signal swing is 3.4V.
http://www.amibay.com/showpost.php?p=20533&postcount=18I need to do this as well but have not since the issue has not been very bad but I have noticed on my A4000 in the real hires screen modes (28 mhz screen modes).
I guess Jens has said this is an official fix.
http://www.amibay.com/showpost.php?p=43314&postcount=32