Originally posted by simX
While APE can indeed cause problems, I don't think we should jump to the conclusion that APE is definitely the cause here.
Do you have too many icons in your Dock (like I often have)? If so, your Dock may just be chock full of icons so it can't make them any bigger/smaller.
Of course, this rarely is the case, but I thought I'd mention it just in case. Would you mind providing a picture of your Dock just so we can make sure there aren't any obvious problems?