I took it into practice mode and I'm pretty sure I finally figured it out! I can't believe I didn't think of it sooner, and I feel like a moron now.
I took Baylor into an offense only practice and just continually scrambled. Time and time again I saw the Griffin "tuck" and slow down. Then...it dawned on me. I tried again and...OFF TO THE RACES!
It only "tucks" when you control your player with the D-pad for some reason. I ran one scramble using the analog and the motion was gone. Every scramble with analog Griffin took off with no slow down.
Weird, but I'm just happy I figured it out. I honestly had no idea why it did this and I have been racking my brain. I usually don't pull my thumb down to the stick until the ball is in the RB/WR's hands or my QB has passed the line of scrimmage. Now I know.