it is not exclusively an issue of W3 TC, but of other methods to minify navigation js. Specilally if you have a CDN also. It seems as though minifying the twenty twelve js navigation would lead to break the mobile menu. I solved disabling minifying js in W3 Tc and using a Twenty Twelve Child theme which optimizes performances. In my case 2012.FFWD by Frank Goossens at http://blog.futtta.be/tag/twenty-twelve/ does a wonderful job with twenty twelve js and css.
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