My findings so far:
I'm using Kipper's HDMI to DVI on a BenQ 21.5" HD PC Monitor. The quality picture is fantastic.
HighGFX modes (at least the 1280x720 which is the only one I've tried) cause the graphical glitches and seem total random. The new SuperPlus 800x600 mode is fine though, no issues at all so far.
I've also noticed some problems with demos which switch screen modes as the Indy2 doesn't seem to be able to keep up.
I'm sure when Jen's finally releases the core update these issues will all be resolved.