All mods and shaders do not reset values for stuff perfectly. This can be easily seen by changing, for instance, shader to blackholesun.inc the text is unreadable.
To demonstrate how it doesn't actually reset everything(which causes problems in the long run) is, first activate inverted.inc and then blackholesun.inc , you can see that some colors stay from the inverted.inc, including the text color. If you would change the shader to something without a sun and no text color change, the sun would stay there and textcolor would be still inverted.inc 's.
Same holds true with mods.
The problem is not with the game, but the mods. :P