The new skype app uses electron and is a quiet good example:

With ambiance the menu looks high contrasted:

Atom is also a good example, to show that it is not only a skype issue:

Visual Studio Code is Electron-based as well, and also affected by this.
It might be a long shot, but have you tried installing gtk2-engines-pixbuf?
Edit: updated! Sorry, now after I updated the ppa this issue is fixed!


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Visual Studio Code is Electron-based as well, and also affected by this.