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Tone disappears!

I had rehearsal last night and in general, it sounded great and I'm really pleased with it. However, I have another issue now. I noticed that the sustain is much less on the 3rd and 4th fret of the E string than any other fret. It seems more noticeable through an amp. Is there a solution to this or is it something I have to live with?
Look at the frets. If they're in bad shape you might need a level.