I just wondered the same thing and ran across your post in the search. I did a google search and found this.
In SCITe, got to Options, and click on 'Open User options file'
You can save the following code in this file, to change the colors:
style.*.32=$(font.base),back:#000000,fore:#12311
style.*.33=back:#C0C0C0,$(font.base)
style.*.37=fore:#939393
caret.fore=#FFFFFF
selection.alpha=75
selection.back=#FFFFFF
colour.keyword=fore:#649bff
colour.operator=fore:#727272
Remove this code and keep the file blank, to put it back to default. Play around with the code to get what you want. I haven't been able to figure out how to change the highlight color yet.
I found this info here:
http://www.scintilla.org/SciTEFAQ.html#BlackBackgroundHope that helps, if you still need it!