I typed in this question on Google because I recently played a 5 string version of my own bass and noticed a difference. Thinking about it I can only assume the sound difference happens when playing with fingers, when you play a 4 string your thumb rests on the pick-up or board and I think this causes a more downward movement with more strength as apposed to bridging the b string which could limit striking follow-through distance therefore producing a slightly weaker (less beefy) sound on the E.
