I can see two possible explanations for what you observed, Kirk. If you were shooting broadheads, the EFOC broadhead is probably bigger than the 12% FOC broadhead and therefore would have more wind resistance, so would decelerate faster.
If you were shooting field points, which would have negligible wind resistance, then it is possible that the EFOC arrow was not tuned to the bow, so may have wobbled in flight. This wobble would not be controlled by the 2" straight fletching. To get by with 2" straight fletching, you have to have a perfectly tuned arrow. Or, perhaps neither of the arrows was very well tuned to the bow, but the wobble of the 12% FOC arrow was controlled by the helical 4" fletch. The helical 4" fletch has more wind resistance than the 2" straight fletch, but the wind resistance of either one would not have as much effect on trajectory as wobble of the arrow itself.