I presume you are carefully reading the instructions on "Skin Deployment" in the wiki
ZWC 5.0 Themes. Did you also notice further up in the same document, that your skin name and directory name must be identical, including case?
Did you try the temporary assessment of the skin using these instructions?
Code:
To test your new skin, add the url parameter "skin=<skinname>" to the normal URL you use to access ZWC:
http://your.server.com/zimbra/?skin=pumpkin
That wiki is a long and complex document. I can't tell you exactly where your error might be, but there are plenty of little details that could be overlooked that would cause a burp. . .post back more details and maybe some of the skinning experts (of whom I am NOT one) can give you more useful guidance.