Jam "separates" in processing
I made apricot/jalapeno jam in August, and I had directions from an experienced jam maker.  She said, after it starts to jell, remove the pan from heat, let it set a minute, then thoroughly stir before putting the jam into your jars for processing. Then the fruit doesn't float to the top. It worked quite well. I used liquid pectin for that batch, too, don't know if that was a factor as well.