Snake45...
Okay, here's something interesting. I just put an RRA mid-length barrel on one of the del-ton upper recievers sold in the equipment exchange (I'm not sure who makes these uppers for them). Anyway, I put a "Wilson Combat" flip up BUIS (elevation adjustable) on it and also put one of the "tall" bushmaster front sight posts in (keep reading...). When I took it to the range, I was surprised to find that with the wilson sight set 3 clicks up from the bottom, I had to turn the front sight post almost all the way down in order to zero it at 50 yards. Turns out I could have just used the standard height front sight post. So here's what I have to wonder... Is this because of a difference in the matchup between the barrel/front sight tower and the upper reciever, or is this because the Wilson rear sight can be adjusted lower than other sights? I really don't know, but it _might_ mean that the wilson sight could cure your problem. Maybe you could contact them and ask...
Hope this helps.