This move by the FIA was brought to their attention by an engine manufcturer and I think it was Mercedes because engine mapping would have no effect on their system if it was based on heating redirected air. It could prove problematic for some of the others and Red Bull, having used it extensbily to great effect, maybe more than others.
There are rumours Renault and Mercedes-powered teams are still using clever engine mapping techniques for aerodynamic effect. http://paddocktalk.com/news/html/story-183675.html
Mercedes you mean? They would have known what McLaren were doing with the engine though. If the example given by the Fia is true and it was hard on the engine to impliment, then they may have asked Mercedes questions about reliability in that area and aroused suspicians. Also I read somewhere that Red Bull sounded strange in the corners and engine mapping was suspected as the cause. We will know soon.