I’ve set up Uv polygroups on a mesh in max (spacing each group 1 quad to the right, shown in the pic below), the polygroups seem to work fine although the colours are not displaying correctly. For example the hands and the arm are seperate groups, but they display with the same colour when i click on frame. Likewise for the feet and leg, and eyes and head. Not a huge problem, as the groups still work but im curious to know what i’ve done wrong. 
I don’t think you’re doing anything wrong. ZBrush just gets lazy when it chooses its polygroup colors. I’ve run into similar situations. They should add some code in so that when ZBrush generates poly groups, adjacent polygroups are assigned contrasting hues. Yellow against purple instead of yellow against light orange, etc.
Just ctrl+click each polygroup, as you did with the hand above, to hide everything else then assign new polygroups until you get the colors you want.
-Dustin
These forums are amazing! Thanks for the info Dustinbrown.
Yeah, manually assigning the colours works, which is cool. Thanks dustinbrown!