Is the CDS market the root of problems in other markets?

No, according to this article in the most recent Journal of Fixed Income:

This article investigates volatility transmission among the credit default swap (CDS), equity, and bond markets, using a multivariate GARCH model. The authors hypothesise that volatility in the bond and equity markets can originate from the CDS market where there is potential insider trading and increased trading activity due to private credit information. However, the authors find little evidence to support this. There is evidence for an alternative view that as investors search for yield across different asset classes the links among the CDS, bond, and equity markets strengthen. Volatility in any of the three markets is commonly transmitted to the other two markets.

I can't find an ungated version of the paper. (If you have a copy of the paper, feel free to email it to me; I would be much obliged.)

Not good news for Chris Whalen and the other crazy conspiracy theorists.