Well, after some testing I figured it out. I was writing the palette ($3F00) after I already set up the PPU (instead of before). So nestopia and fce ultra accepted the writes to $3F00 after I set up the PPU, while Nintendulator and VirtuaNes didn't. So I got a few questions now.
1. How would a real NES work (would it allow the writes after setting up the PPU, or would it not?)?
2. I know that it is possible to change the palette values after setting up the PPU, but my question is how? What was I doing wrong? And why did my writes to $3F00 not work after setting up the PPU? thx :)