Now sorted via PM, but just for anyone else this was solved by editing the functions.asc file located in the C:\Program Files\Apophysis 2.0\Scripts directory to contain this:
{ Functions and procedures for use
by other scripts. }
procedure CalculateColors;
{ Spreads the color parameters evenly }
begin
for i := 0 to Transforms - 1 do
begin
SetActiveTransform(i);
Transform.Color := i / (Transforms - 1);
end;
end;