For some reason, Layer 6 is all messed up color wise. I tried it out with other palletes, and the lower stuff is fine. It's only layer 6 that's a problem. Here's an example.
Layer 6 pallete problems
as far as the pallete goes, it always has done that. In the game it looks fine, but it can look terrible in the editor.
Also, FYI... It seems to be mainly linked to the tiles themselves. How do I know this? Set up a transparent layer on a screen, move to another screen then come back, just in case you need to fix the colors, then go to the Edit Tile screen (where you can actually EDIT a tile, not select one to edit). Go back to your screen, and.... The colors should be messed up. I believe it might be messing up when loading CSets there, so..... The only way to fix it is to close out the editor and go back in.... :/
I actually know all of the issues/solutions that you mentioned, and I couldn't get any of them to work. But when I loaded it later, it had fixed itself, so I dunno.....
Try pressing "B" to rebuild transparencies, That should fix the palette problems.