Hiya,
Every Amiga motherboard is a bit different.
With my set-up I've found that it's only happy at a max resolution of 800x600 (SuperPlus), if I try to go to 1024x768 or 1280x720 then it becomes glitchy after it warms up a bit (maybe 10 mins usage).
Some people have fixed this by installing fans/heat sinks and for some people it works fine without any modifications, like I said all 1200 motherboards are different.
To be honest 1024x768 and 1280x720 is a bit much of AGA, 800x600 is perfect on mine but unfortunately the Mrk2 no longer supports SuperPlus. I'm currently running mine is PAL 640x512 and 256 colors, if Jens ever adds SuperPlus mode back then I'll switch to 800x600.