I haven't had the problem myself, but I know a friend was having a similar problem. I recommended using Journal Watcher which is a website you can upload your zip of icons to, and it'll upload them for you. I switched to that because I switched to a Mac laptop, and it was simpler I find that with JW, as long as I don't try to upload multiple zips at the same time, it does a good job, although I admit, I haven't needed to upload bulk icons in a few months. The friend who was having trouble with the uploader not uploading everything, though, said JW worked out great for her.