I just found that unchecking the Transparent option for the Temperature Above Freezing tray icon changes the icon from black-on-red to the correct color, even without clicking Apply or OK. I’m wondering if this issue has something to do with the fact that I chose the same color for Background as my system uses for the tray (that color being 211/211/211), and kept the Transparent option enabled.
That’s normal. Your changes will be undone if you click the “Cancel” button.
I tried that on my computer and the colors still displayed properly.
I’d suggest you keep the transparent box unchecked since your system tray is a solid color. I’m not able to reproduce this issue, so it’s going to be hard to attempt to fix it at this point.