That's because your prefix-free plugin only runs at pageload. Since the prefix-free plugin parses each stylesheet in your document on pageload, the square is rotated 20deg.
After pageload you give the css property transform
another value with javascript, but the prefix-free plugin does not know that. So you should 're-run' the prefix-free plugin after each interval.
EDIT: it seems I do not need the plugin for jQuery 1.8.0+, which auto-prefixed the css properties already, so thanks for making me search again. (anyways I still don't know why it did not work, but it does not have to now)