There are plenty of Focii and a few Mondeos that have had the whole std airbox removed and just have the
ecu sitting in the engine bay near the battery and i haven't heard of anything like this happening, and they work them hard even in the heat... but it could be, it could a number of other things too... but take the spacer out and see how it goes, another thing would be to de-tune back to stock and see if that makes a difference also...