Different thing. CSets 12-15 are reserved by the system and can change arbitrarily. The colors labeled as "Sys. Color" in the subscreen editor are safe to use, but they don't correspond to any specific palette entry.
Then I may encountered a bug. I'd have to go back and look at very old versions of TGC to be certain, but I recall using swatches from 'System Colours' on my passive subscreen, that always changed to black, if an enemy off a specific list was on a screen. I recall that all BS enemy types did this, and a few other enemy types, including the Gleeok.
I was using system colours for counter text, in that case, and believe it was in the green, cyan, and magenta shades that this happened. I changed to other colours (other than 'System Colours') and never again encountered the problem.
If you would like, I can find a version of the game that had this problem, and send it to you.