You know I've got a skin set that's about 7mb by the time all the 60 skins files are in there with the preview skins (that's what takes up alot of the bandwidth when uploading) and realised this was never practical for using the skin uploader, so, I package these skins in two ways - I package without the preview skins and then have a separate zip file for the containers and skins previews to be uploaded via ftp or even the file manager to that folder.
I have asked in the core team enhancements several times for the skin preview file to be able to be a .gif or .jpg - at the moment it's only .jpg and I know in some instances I can cut the files size down without losing quality by 50% and that I think is a resource saving option.
Also, several people package skins and containers together.. which can make the upload more intense.
How about you simply split the skin up and add a few files at a time and upload - eg.. 1 skin, the files it needs, and then create another zip - same name with the other files.
Sometimes there are issues with DNN and other times server issues.. you could also look at setting the web.config file to not time out with larger file uploads.
Because I work in ftp method and ascx mode - I rarely use the skinuploader, mainly because of time it takes zipping them up all the time and uploading , so if you have ftp access, have you tried to ftp to server and see if they appear.
Nina Meiers