facing the same problem!!
Minify not working and cdn not working when using w3tc / wp super cache with wordpress seo. As soon as I deactivate wordpress seo everything works.
Wordpress SEO version 1.4.9
W3TC version 0.9.2.11
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Gautam on "[Plugin: WordPress SEO by Yoast] Conflict between W3TC and Yoast SEO"
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