Is it possible that the draw cord could be set too short also?
Yes that is possible, because coming up too fast can make a rest drop too fast resulting in not enough guidance. Every dropaway that I have seen must have the proper timing, some more than others. I have also read about bounce back. If you get a chance to see the video from Vaportrail's Limbdriver dropaway rest, its really neat as it shows the rest dropping just barely before the fletching passes by.
By the way, I use a Schaffer on my Bowtech Patriot BUT have the old prongs and found that 1.5" to 1" just before full draw works best for me and I really like the Schaffer. I'd say the newer prongs might be more of the problem though.