Track pane and Transforms new icons are derived from the original Mercury. So if you have a theme based on Tungsten, you now have some Mercury buttons.
 
Easiest way to fix, I think, is to open two versions of them Editor, one for Tungsten and one for your theme. Right click and copy the icon from Tungsten and paste to the icon in your theme.

Theme Changes for the Track pane can be found in Theme Editor under:
Track Pane
 
But the changes to the CC types are not PNG files, but Colour Choices found under:
Track View> Focus Track Backgroud
Track View> Focus Track Text (This is not picking up right now, but will in the 17.05.2017 release
 
http://forum.cakewalk.com/FindPost/3601581