A lot of times the home replacement you have has the option to do that in its settings
After flashing your theme, go in to the Galaxy S widget settings and change the colors of the indicator. It will fix the problem. Not sure why it happens but i had it with the GB theme and the Galaxy S theme, change of colors seems to do the trick.
I tried Gimpsource for a day or so (escaped back to Sourcery really quick) and had the same issue there as well.