We are noticing an apparent issue with the Domain Mapping plugin breaking CDN redirects.
We have set up a few test sites on a 3.0.1 multisite network. We use the OSSDL CDN Off-Linker plugin to create the new URLs for CDN items.
So, for example, the hostname for images ends up being cdn.mydomain.com, rather than mydomain.com.
When we add this plugin to the mix, the URLs are not rewritten by the plugin any more. So, for example, you never see cdn.mydomain.com and more...just the original hostname.
However, this problem does not seem to happen when using Donncha's domain mapping plugin.