My changes seem to appear when I re enter zbrush, however when I pick them up they are not applied?!?
I thought polypaint worked with zapplink no? Any ideas as to what is going wrong?
bump! still having this problem 
post some pictures, could be that your rgb intensity is real low
also please explain the problem in detail a bit more
Do you happen to be on a 3D Layer? The Zapplink projection will only apply to areas that have already been painted if so.