I'm guessing that you were predicting cook time based on weight, and since it was only 3.5#'s, you thought it would cook quicker. Cook time is based on the thickness of the meat, not it's weight (though weight is somewhat related to thickness). At 3.5#'s, what you had was probably a partial flat (though it might have been a point). A 7lb partial flat that was the same thickness would have taken just as long to cook.
Additionally, the lower the chamber temp, the longer the cook time. You were set at 225, so it will take a loooong time. 14+ hrs isn't outside the realm of possibility.
Lastly, your MES is thermostatically controlled and runs in cycles. The heating element doesn't just run up to 225 and then hold there. Basically, it's binary and is either "on" or "off". It switches on and your smoker starts to heat up. When the internal temp probe registers 225ish, it shuts off and your temp starts to drop. At some point, the element kicks back on and the temp is brought back up to 225ish once again. Element turns off again, rinse and repeat the cycle.
What this means is that while your set point was 225, the average cooking temp could have been down at 210-215, which would increase your cook time even more.