For anyone still modifying their colors file please note that the latest release (v2.65) has added another line to the colors file to style the new tooltip. The line you need to add is:
atom-tooltip-bg #fffffff (or whatever colour you prefer)
Also, it’s worth mentioning that the ‘name’ file (the one that lives alongside the ‘colors’ file in each theme folder) is finally worth editing as Roon now respects the content of that file and reports it within the app. In other words, you can now name multiple theme files within Roon that report their own name rather than just saying ‘unknown’ (see below).
If this is definitely the case then there’s a discrepancy between your modified theme file and the standard one, so you’ll need to find what’s different. In the past, when confronted with the same problem, I put both color files (modified and default) into Excel and put them in alphabetical order. It made it much easier to see the differences.