I tried the Google favicon and Phoca favicon and got the same results. Favicon are mostly small images (16x16) so they are resized to some large image, if there are copied into the desktop.
Maybe there are some favicons which contain more images (small, medium, ...) so then there are used on desktop, but Phoca Favicon only creates one image, which is used in URL bar or as bookmark
I will take a look at it. Adding more images into ICO file added into feature request list.
Jan