I just (now, prior to this post) played on my small 15 watt practice amp and the sound coming off of all 4 strings sounds equal. So, based on what you guys have said, Im thinking it must be an amp issue.
Just lower the E side of the pickup.
if the sound coming out of you bass is currently balanced well then i would NOT adjust the pickups to fix this - it will work short term, but then if you want to use someone else's amp or backline one day you'll run into the reverse problem. not to mention it's not really fixing the real problem.
i agree though it sounds like an amp eq issue. i would play through a few different amps first if you can and see for sure if the sound coming out of you bass from the current pick up heights is even and balanced. when you tested it on a small amp, it might have struggled to produce the lows from your e string and over compensated for the imbalance.
if you have a mini disc recorder, or mp3 recorder or PC recording program and can plug directly into the device and record it, then listen back on good speakers / stereo that you know well to be balanced - that will give you a good indication of how balanced the pick ups are.
once you have a balanced signal coming out of the bass, start with a flat eq on the amp and adjust to suit your taste. i personally prefer the subtraction method, by taking away what there is too much of rather than boosting what there isn't enough of, it gives a more natural full sound rather than an artificial scuplted over-eq'd type sound. you then might have to turn up louder with this method. also try adjusting the tone knob(s) on your bass to see if that helps to find your sound if the amp and eq on the amp aren't quite doing it for you.
also, it's very common for bass amps and bass cabs to have purposely designed eq curve spikes around certain frequencies so that it sounds "good" and "bassy" and "has nice low end" etc. sometimes this is done in an unnatural way, and can become obvious depending on the combination of equipment you are running. nothing you can really do to fix this but try and eq it out with on board eq, tone controls, and eq / tone pedals.