| ppanousos,
Here are a few things to check first. If these suggestions don't work, reply to the post and we'll try a few other things.
1) What kind of pickups do you have? Do they have blade magents or individual pole pieces for each string? (if you don't see any individual poles on the top of the pickup it probably has a blade magnet). Is your pickup height properly adjusted? If the pickup is not close enough to the string (or the individual pole piece is not close enough) you might get a muted sound. A low pole piece is my first suspicion.
Conversely, if the pickups are too close to the strings their magnetic pull can mess with the vibrations and possibly cause strange sounds/muting. Of course you did already say that your action wasn't too low...
2) When did you last change your strings? If the strings are old try a new set. If the strings are new, did you change gauges? Though I have never heard of it causing a muting problem, it could be possible that heavier gauge strings don't fit your nut slot properly on the E string, causing it to sound muted.
Check how the string fits in the nut slot. If the slot is really wide and the string doesn't fit well that could be a problem. Another problem could be if the slot is too narrow and the string doesn't fit in properly, or sits too high on the nut.
3) Do you have active or passive pickups? If you have active pickups, replace the batteries.
4) Does the string sound muted on all the frets? Just in the open position?
5) Is the bass in standard tuning?
Let me know how it goes...good luck! | 
