Some themes add
.tmPreferences files that change what theme class name is used for various file types. This is most likely the original issue you ran into when the icons were missing. The preferences change what the themes need to use to set the icons for various file type, and if the theme doesn't provide an icon for that, the icon is missing.
I am not sure why the Soda theme would be showing black icons. Can you check in the Console and see if any errors or warnings are reported?