We'd need more info about what screen is open, are you using bobs or sprites to draw... Have you tried using GET SPRITE PALETTE etc.
There are some nice palettes storing functions in AMCAF I've used several time to avoid some of the "quirks" in Amos's colour commands. This is largely because of having created a "variable" palettes set for my loading screens though
What I have done apparently is used Colour <n>,<data> that matches the palette originally in the correct order of objects.abk itself. It works in such away that even if all the colors in palettes in objects.abk is set to $000 for all the 16 colors and sprite look like black spot in the game it would still display the colors and show the sprites correctly because of the 16 colour codes I have used. I actually used them as reference when I accidentally screwed the palette colors in my object.abk and have it saved...I wrote down the color patterns again and went manually and refixed them in objects.abk and I am pleased on that.
So what is the point of this silly babbling? That I love AMOS and it is a truly fun programming language...this I am not denying. Putting that aside I removed sprite from my game all together and instead using paste bob which also means I introduced new set of bugs but I am fixing it slowly.....I am working on making sure there are no trails behind the character when he walks, make sure it does not destroy the graphical display of the other bob underneath it and to show animation and so on...working on all of that actually...truly fun...but I what discovered when using bob instead of sprite is with bob it looks smoothers....but I could be wrong. However, thanks to the concept of paste bob I can plot as many bobs as I want without fear of limitation and with my own internal collision detection instead of the predefined one in AMOS...I am truly happy. Progress of this game is growing bigger and bigger.
Here is another thing I learned now as I am typing this...thanks to the Colour <n>, <data> coded in my engine I can play with it..to give the screen fading out and fading in effect. I can write my own subroutine that says fade out...and slowly the entire screen turns pitch black as it slowly and progressively fades the colours to $000 all together. When I execute the fade in subroutine that I will write down...it will increment the colors to the maximum value for each color command one point at a time giving the illusion the screen is showing again. With this I can make the screen go black...do all the drawing that makes it look AMOS like or ugly or whatever...and when all the drawing is done...fade in the screen again...and poof it shows the new level pattern and so on.
Ones I am done with all the bug fixes I want to study and learn Ctext as I am intending to replace all the fonts of my game with better and make new sexy TITLE font.