On the top 3 strings (though more prevalent on 3rd, less on 1st) I get a weird watery fluctuating sound. It's like when your tuning with harmonics and one string is about 30 cents out from the other, but this is a fretted note on one string.

I thought it might be my intonation but according to the tutorials here it's almost perfect. I thought it might be pickups so i exchanged both of them but it's still there. I don't think it's the nut since it occurs on all frets.

I use heavy gague D'Adario's 12-54 on an MTM2 with an FX Edge III bridge. It's floyd rose style but fixed.

Thanks in advance.
@cainmd the guitar has no springs

@ethan_hanus but i still heart this effect when the strings are open, especially the 3rd.
I know, same with mine, if your referring to the 3ed string as the G string, it gets this buzzing type sound when open or fretted anywhere before the 15th fret. Won't innotate worth a damn, and sounds nasty when trying to do solo's.

It's the frets, either the fretboard has warped slightly, like on mine, causing the frets near the 15th fret to be unlevel with the rest, or you've just worn them down so much that they are now unlevel.
Hmm well that's unfortunate since the guitar only cost $300 to begin with