Ok this is my problem *Sigh
I was working on Skullman and recently got the icon for him.When i add the icon it shows up perfectly. I save and reopen and the Icons Palette is not in the "Palettes" (it didn't save, i don't know why) and the icon is forced to use 1,1 Palette.
Here is an example
(If i add the icon and have 100 Palettes save and reopen im down to 99 for example).
EDIT:
I just merged the icon Palette into Palette 1,1 (Top colors are icons, Bottom colors are Characters sprites)... I don't like doing it like this but it worked if anyone has a better fix to separate the palette i am all ears.