@JakubMisek until now, I did not find any further issues with colors.
I am afraid I was not precise enough the last time, I am sorry for that. the correct issue is that PHP variables were displayed as regular text colors (I am using "Dark (Extra Contrast)" scheme, so they stayed white. I could adjust the PHP variables back to lime using your advice, thank you very much for that!
If I change back to "Light" scheme, they are displayed like regular text in black color. (Changing back to "Dark (Extra Contrast)" the variables will still be displayed in custom lime color). Maybe this issue was triggered in combination with the recent 16.10.4 update?