The low E string goes down in pitch, sort of like when using a whammy bar. This is pretty noticable when playing the first 4-5 notes of Cliffs of Dover as the low E is held whilst playing the opening phrase (started by the bending of the high G). Like a whammy bar, when the string at that note is returned to its rest position, the low E string is still intonated.

I've had the guitar for about a year now and this has been the only problem I've had with it... Can someone please tell me what the exact problem is and how I can get it fixed?

Cheers in advance.
Maybe the whammy bar is in full floating mode? That sounds like something that happens to guitars with floating tremolos.... I'm no trem owner though.

86% of the people who frequent the "Electric Guitar" forum would say that they have played guitar for under 5 years.
How is your bridge adjusted? What's happening is the added pull of the bridge from the string bend is causing the bridge to be lifted, effectively bending the lower strings. To fix this, either tighten the springs in the back of the guitar or add some more springs to it. Max it out if needed, that's what I did.
you can always remove the E string and scratch some pencil lead of a pencil and put that on the nut ( in the E slot ) , this should improve tuning stability .
Orange Enthousiast.
That'll happen on any tremolo to some degree, it's physics. Bending a string increases the overall tension of the strings, if it then becomes greater than the tension of the tremolo springs you'll pull the bridge forward.

On a non floating strat type or non-recessed floyd you can eliminate the problem by increasing the spring tension either by titghtening the trem claw screws of simply by adding springs. Basically you make the spring tension so much higher than that of the strings that it's simply not possible to get enough of an increase to affect the bridge with everyday playing. It'll make the trem stiffer but won't change anything else, seeing as the bridge sits flat on the body anyway. Won't work on a Floyd because that relies on the two tensions being equal to keep the bridge level, if you increase the spring tension on a floyd then you only have to increase string tension to match it so any bending will still result in string tension being greater than spring tension and you'll pull the bridge forward as before.
Actually called Mark!

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