I tried the updated version on my C64 Maxi but it still has the annoying color shifts when scrolling starts/stops.
What display settings are you using? I use European PAL 4:3 CRT on my C64Maxi and it looks superb on an HDMI TV - I've played through the whole game and haven't seen any of the colour / scrolling issues you mentioned.
It doesn't matter - every mode I try, North America, Europe, CRT, or not and I get the color shift when scrolling stops.