Thank you for bringing this to my attention, I'm looking into it as I type this message.
There are two things that come to my mind that could be the problem:
1.) Gale doesn't index images and that could be the problem. In some cases it will grab exact colors, and other cases it wont. When you save a palette in gale with a un-indexed image it gets a lot of other unneeded colors. Or it could be a palette file that only Gale can read.
2.) .PAL files are a bit messed. I've had troubles with .PAL files before. I'm going to look deeper into this for you and edit my post/PM you with the results.
EDIT: Ok, I've narrowed it down and it is because Gale doesn't index images. If your tile set has over 16 colors, it will load with a palette like this, which is way too many colors:
So you'll need ifranview.
1.) Open your tile(s) in ifranview.
2.) Go to Image -> Decrease Color Depth
3.) Select 16 colors and hit OK.
Now when you reload your tiles in Gale, you'll end up with a much for specific palette, like this:
Now save the palette and try it again in A-Map. It worked fine for me when I just tested it.
Sorry that gale is turning out complex with palettes.
For your multiple entries error, the fix is in the FAQ.
EDIT2: WOW, I checked the palette after I loaded it and every color is darker. For now I recommend not using Gale for palettes. I didn't realize this palette files it saved would do this.
I mentioned this in one of my "Did you know" tips; you can paste a tile that you want recolored into another image that's indexed. It will automatically change it's colors. BUT there's two things:
-You have to be really careful because sometimes it will give the tile you just pasted bad colors.
-If it's over 16 colors, it will usually not come out the way you want since it has so many colors. You can try it though.
You should try this if the image your pasting the tile to has similar tiles, like a cliff into a rock tileset.
I hope I understood your question correctly. >_<
Anymore questions, please let me know.