I had some pixel corruption when I was creating the 1280x720 mode, but after increasing the pixel clock and changing the porch settings to get the correct h/v clocks again, the problems disappeared. I don't know if it was the Indivision or my monitor that caused it, but if you have the issues, you could probably improve it by fiddling with the VGA mode.
Edit: I think the drag-screen-down problem is related to the black screen I get after changing modes some times, since it will change to my HighGfx WB mode when I drag down the PAL screen. Since rebooting the Amiga is the only way to get a picture back, I assume that the problem is in the MkII, perhaps an unclean clock as you mention. If I had an oscilloscope it could be useful to watch if the clocks change in any way when this happens.