I'm not sure I understand what you mean by "sequence pane colors". In TestStand 4.0 you can change the colors of the pane where the steps are. Right click in your sequence pane and go to Step List Configurations>>Edit Step List Configurations... Then you can click the Edit button and then the Fonts and Colors tab. There you can change certain colors.
Since you mentioned the SequentialModel.seq then maybe you are talking about the sequence icon colors. For instance if you look at All Sequences in the SequentialModel.seq then you'll notice that some are green, blue, grey, purple, and red.
red = entry point
purple = engine callback
green = model callback
greyish = configuration sequence
light blue = normal sequence
The order doesn't matter except that the entry points are usually first.
hope that helps,
