Originally Posted by Herrlster
When I play the open E and fret the E on the A string or D string, I can hear a "wavey" sound, indicating that the E string is out of tune.
What I quoted is a bit confusing to me. Are you literally doing what you typed or do you mean "When I play E on either of these 3 strings".
Either way, the problem is sympathetic vibration. If you are doing what you typed, then that is to be expected & the waviness is you hearing the beats due to minor imperfections in your intonation.
If you meant "When I play E on either of these 3 strings" then something on the bass is vibrating. My first step in trying to isolate the problem would be mute the E string so it can't vibrate. Do you still hear it?