What were the weather conditions for the two times being compared?
I haven't used a JB4, so I don't know what to expect there. But yeah, if conditions were equal I'd have expected a lot more too, assuming it should be running significantly more boost with the JB4.
I'm very similar to you, 2008xi 6MT. Bone stock I also ran a 13.9@98 my first time out. As soon as I installed the Cobb that same night I ran 13.6@101 with no other changes. I started playing with E85 before making any hardware changes so it's hard to compare any of my results after that. But I will say I had really good results with E85 :-). Not sure why you didn't get more...do you have any logs?