There was a time when uploading a non-image file (such as a zip) onto upppy would replace the original file. Clearly, somebody uploaded a different skin with the same filename and it replaced the real one.
As far as I know, peppy has never released the current spinner circle graphic, so the old one is the only one you'll find anywhere. The template skin is there so you can reference the filenames and dimensions, so it shouldn't matter which version of the graphic is in there, although I do agree it would be nice to have it updated. If you want the current default spinner graphic to show up when you play, you could always delete spinner-circle.png from the skin.