Compounding gel coat problems

I washed my boat with boat soap, and powerwashed. This removed a lot of deep stains. I compounded the red gel coat hull of my Scot this weekend. Except for the normal wear and scratches and UV fading where the boat numbers were it looks show room new. I then tried the same on the once ivory colored deck (more white now compared to the original color under the non-slip strips now removed). It seems the compounding solution even stained the deck. I was using a West Marine heavy duty compounding solution with a wool compounding bonnet. Do I need to use a mineral stain remover, sand with a 500 or 1200 grit wet sandpaper, compound again after doing that? Does anyone reccommend another solution to bring "some" of the gelcoat deck back?