The number of files did change, but only went up. Anything from older versions still exists and gets replaced by skins from newer versions. v1.0 hasn't had any changes from b1.1.5 other than cleanup (which was just removal of comments and adding of new ones) and packaging.
And I know you're not bashing the work or anything
I'd like to fix any problems you're having.
If you have a chance... If you could copy the .skin file to that incorrect skin's folder and to zip up files (if you're on Windows XP or Vista) you can right-click on a folder and choose "send to->compressed zip folder". That will give you a zip file with the same name as the folder. It just makes it easier for me to see exactly what your settings were when you created the skin as well as what exactly went wrong.