why does one note sound louder than others?

[fokof]

When you play your bass unplugged , does the E stand out compared to other notes? ( When you play everywhere )
If not , You'll know it's not your bass.

I have a "dead note" on all my basses , a note that is softer than the other , usually around "D" on the G-string.
There are notes that stand out too , on my fretlesses , it's very obvious , but nothing dramatic.
It's normal that notes are not perfectly equal on a bass. ( unplugged )

I'll bet too on room acoustics......

 

[blubolt]

I was wondering if maybe a Boss Bass EQ pedal (or some other brand) would allow me to notch out that frequency and tame this lion? has anyone given that a try?

 

[TimmyP]

Does this happen direct as well, or just through your rig?

Many cabs have a hot spot around 160Hz. This is two octaves above your open E, and would be likely to accentuate the Es. Some also have a hot spot close enough to 80Hz (an octave above open E) that this might pump up the Es as well, although usually it will accentuate Ds or Cs more.

 

[groooooove]

usually thats the room- sometimes youll have a rehearsal room where certain notes make a snare drum go insane..

but it could be countless other things. construction of your instrument.. pickup height.. your amp/cabs.. ext ext.

have you tried playing with a (good) compressor?