When I try analogous operations using PDB files 1kaw and 1eyg, the coloring comes out as expected.  I have attached a .cxc file with the commands I used.  Maybe you could try that file and see if it works for you, and if it does then compare it to the situation you’re having difficultly with.

Without access to your data files, the only thing I can offer is that you should ensure that you are displaying / looking at the chains that MatchMaker used in its matching and that are associated with the alignment.  Other chains will not have their colors changed.