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Here is the fixed subroutine:

sub GetSquares toshuffle:
  my sqr piece;
  // determine the squares the pieces in the given set are on.
  // the result is left in 3 global arrays:
  set left array;  // on left board half
  set light array; // as well as sorted by shade
  set dark array;
printr $space;
  for (sqr, piece) $space:
print . iter . #piece #sqr;
    if match var piece #toshuffle:
      if < * 2 file #sqr lastfile:  // left half
        push left #sqr;
      endif;
      if == color #sqr 1: // distinguish by shade
        push dark #sqr;
      else:
        push light #sqr;
      endif;
    endif;
  next;
print "got it";
endsub;

The actual fix was changing #piece to var piece in the conditional if match var piece #toshuffle:. There are subtle differences between these two ways of getting the values of variables. The way you were doing it embedded it into the line during pre-processing, and the problem with doing that was that its first value was -, which is also an operator. Changing it to var piece made sure that it treated the value as a string at the proper time and not as the minus operator.

I changed another line to use the color operator, because this might be a better way of doing what you want. This returns the color index associated with the space. Looking at the color values, I figured that the number 1 was being used for the dark squares.