skins used by the site should exist at /Data/Sites/[SiteID]/skins where siteid is usually 1 for a new installation
the ones under /Data/skins is just a catalog of skins, when the site is created it should copy them to /Data/Sites/[SiteID]/skins
but something could have gone wrong so check and see.
also make sure you understand about working with the source code, and how to package a build, maybe compare the files from your package with the official release package to see if you are getting the right stuff.
actually your error makes me think you re-compiled the already compiled release package instead of the source code, that will break things
but you did not post much error detail, or stack trace