Can javascript cause a supplemental issue?

fixed activeX issue, now my site is gone

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My site lost most of its indexed pages in G. I'm not sure if it has to do with the recent update or if my ActiveX fix may have triggered a penalty.

I implemented the swfobject.js fix and Apple's quicktime js fix for the recent embedded content issue in Explorer. Could this be at all related? I noticed G spidering the .js files. Does that count as duplicate content?