Sorry for the late response. I haven't checked in on this in awhile.
From the looks at it, after loading the palette in your block editor the palette gets really disorganized, which honestly shouldn't be happening.
When you save the palette from Photoshop the palette should remain the way it was viewed.
Here, I'll show you how I organize my palettes when things aren't the way they should be. It's very simple.
First:
I use graphics gale for this.
Download link.
Start up graphics gale and load your INDEXED image.
Second:
In the palette viewer, click the downward arrow and select Uniform Color.
Like so:
Third:
Select your image from the list in the box that pops up, and then click extract.
Fourth:
You will notice that your palette is now loaded in the right box. From there you can edit your palette freely.
By that, I mean you can drag colors and organize them as you like.
Just drag whichever color you want to be transparent to the first color.
Fifth:
After you drag you will notice the colors swap places in the palette. Click "Apply" and then save your image.
Now open the image you just saved in photoshop or your palette saving program and re-save the palette.
If you still get this problem, my only thoughts would be that you're loading the wrong palette in the wrong directory.
Again, sorry for the late response.
ALSO/// DO NOT SAVE PALETTES IN GALE. The colors darken.