#1
Hi fellas,

the time has come, again, that I request your aid. I have bought myself an awesome guitar a few months ago with a floyd rose and it was all ready to play and already tuned in Drop C, but after a while, of course, the tuning went a little off. So off, that I had to remove my tremolo locks at the top of my guitar. After that I retuned and everything seemed to be in order when I encountered the following problem:

Even after I tuned all my strings right on the spot, the frets seem to be off a lot. Every tone until up to the 15th fret was alright but further up they became off more and more, meaning the first string for example was a perfect C, the 12th fret was a perfect C too and further up the notes lost almost half a tone.
At first you could barely hear that but over time it got worse and I wanted to retune it. Now I have the problem that it's almost half a tone too high at the FIRST fret already and almost half a tone too low at 15+ even though the string itself is right on the spot.

I know that these guitars aren't quite made for this kind of low tuning, but I have thick enough strings and it worked well enough already, but now it's becoming worse and worse.

I feel like I am missing out on a very essential and obvious mechanic that kind of determines the purity of the frets? Can anybody help me?
#2
You're not intonated for that stringset.
Fix that and you're good to go.

Also make sure that the butt-end of the Floyd isn't sticking up in the air. If it's not level, you're going to be slightly sharp all over the place.

Hopefully your guitar isn't a 24.75" scale -- that's going to be slightly tougher to intonate properly with thick strings (you didn't mention a gauge, actually) and a Floyd, but it can be done. And remember that you should be setting up the Floyd so that you can tune with the fine tuners. I usually work with skinny strings (9's) on Floyds, so I'll cheat a bit and let the fine tuners out a bit over the midway point; I rarely have to deal with sharp strings, but I'm usually compensating for strings that are slightly flat.

One thing I've noticed with some lock nuts is that when you screw down the locks, the strings will go sharp. If this is happening, put your fine tuners slightly less than half their travel toward the middle. That way you can let the fine tuners out a bit and bring the guitar down to standard tuning. Then, as strings stretch and go a bit flat, you can screw the fine tuners in, and you have plenty of travel before you have to pop the top on the locking nut again. By that time, you probably need new strings anyway.
#3
Yeah, get your intonation checked. Take it to any local shop and have the tech fix it up. Should take like 20 minutes. And make sure you're using heavy enough strings for that tuning. I use EB Skinny Top Heavy Bottoms, which are 10-52, with a Floyd, always between D Standard and Drop C tuning. And stretch the absolute shit out of new strings before you lock down the nut. With that stuff squared away, your tuning should be very stable, assuming you've got a real Floyd, and not one of those god-awful licensed ones they put in cheap Jacksons. I put my Schecter Hellraiser with a floyd in Drop C, and I can do whammy dive bombs for like an hour straight, wrenching on the bar till I damn near rip the strings off, and it doesn't come out of tune.