I'll kind of take you through the diagnosis...
If you're dealing with inconsistant tone on a single string you can normally rule out fret wear, high frets, low frets, or general neck warping... since this normally will affect more than one string and generally in just a few spots... So we've ruled out fretboard or neck problems... Now we look at the fact that it can't be the neck or frets... When dealing with string noise you have four things to look at... Neck/Frets, Bridge, Nut/sting retainers, and the string itself... Now... since we've ruled out the neck/frets we look at the others... The bridge, depending on what type of bridge you have will alter what can possibly be causing the noise... A hardtail bridge or a Strat style trem bridge may be causing the noise because of a loose saddle... Or it could be a matter of the string being incorrectly installed or shifting in the string seat and causing the string to vibrate inconsitantly... As for the nut/string retainers it could be a few things... one is if your guitar uses string retainers, also known as string trees, to pull the strings tight to the nut... the retainer may have raised slightly... releasing tension on the nut on your e string and causing it to vibrate eratically..... the reason this only affects one string is because the retainer has only loosened enough to release enough tension to affect the e string... once the retainer loosens more your b string will eventually soudn that way too... As for the nut... it may just be a worn nut... which is unlikely..... normally a nut won't wear as much on the e,b, and g strings because they're made of gut wire... which will cut through the nut instead of wearing a lateral slot for the string to vibrate inconsistantly in... So we can rule this out as well... Then there's the string itself... which may need to be changed... which in turn will take care of the incorrect seating of the string in the bridge...
So now we're left with the string retainers being loose or the loose bridge saddles.... One way to check to see if it's the string retainer is to press your finger down on the string (light tension) between the nut and the retainer while playing an open note.... Once the note is played let it ring for a moment... then let off... if the sound goes away when your finger is pressed on the string you need to tighten the retainer... If it's not the retainer... then there's a good chance it's a problem at the bridge... Tighten up the saddles and see if that helps... I suggest changing the strings either way... Normally when my tone goes sour I just change strings while I figure out what's wrong with it... sometimes the string change is all that you need.
