I just found out, that when you use 'Type Shapes' creation mode, along with 'Colour Switcher' affection, turn 'Key Drawing' on, press 'X' (Foreground/Background), and then start to draw, alchemy changes your 'base' colour of whiteness. It can't be undone by any option, even restarting, or loading new image doesnt helps. It seems that it changes the 'base' level of program's whiteness, since when I tried to draw with pure white later, it painted the changed background colour.
Screenshots:
Every image is taken after a mouse click.



The way to deal with it - make purely white image in Photoshop, Gimp etc., and use it as background image.