Simple reason northbound.
When the exit lane to the LIE is slow, a lot of people who want to exit will ride the faster left lane, trying to figure out a good time to move right. Before the bridge, much of the on-ramp traffic doesn't want to exit to the LIE, and moves left to stay on the BQE. Add trucks to the mix, especially when they have to break hard to avoid slamming into someone who cuts in front of them, and they have to run through several gears to get up hill.
This maneuvering slows everything down.
There are lots of places where this happens.
Don't know about southbound though. It always seems faster to me.