Well, I'm embarassed to say that I do not understand why this happens. Everything is the same, from the css to the navigation provider version as well as spmenu.js. The only 3 differences that I'm aware are :
1. DNN version, which I'm pretty confident that doesn't affect much. DNN skins are supposed to work fine in both version of the framework.
2. When I installed the skin on localhost, I had to delete the register tag for Data Illusion Feedback Server. This, however, doesn't affect the appearance also, I believe.
3. The content of your site. This, in my opinion, is the most possible cause.
Try creating a blank page and see what happens. If that problem is still there, I'm afraid this has gone over my ability and you should ask another DNNer who has more experience in this.
Good luck,
Duc