CoherentGT uses a different low-level graphics library, which we call internally Renoir. Although most of the HTML content is rendered identically to the existing browsers, sometimes for performance reasons we choose to deviate and things look differently.
For prototyping your UI we recommend GTPlayer, since it would render the content like in the actual game.
But sometimes those deviations may be undesired and a bug. To investigate your use case we would need a sample or the part of your UI to reproduce it. This will be best handled in our support system, so please open a ticket there and send us some more info.