Content Pipeline importers and processors written for XNA Game Studio Express 1.0 will not work in XNA Game Studio 2.0.

If you are referencing a custom Content Pipeline extension library (SkinnedModelPipeline.dll), make sure that it supports XGS 2.0. If it doesn't, then you can either upgrade the project that built it (if it is yours), or obtain an upgraded library from the vendor (or whoever) you got it from.

The reason I mentioned the version is because references to 1.0 versions are ignored by the 2.0 content pipeline. You said you already have a reference to the DLL, which should be enough, but if there's a version mismatch then that reference would be ignored and the importer still would not be found.

Can you double-check that the reference is in the right place? You need to add the reference to the GameProject\Content\References node, not the GameProject\References node. The separate References under Content are for the Content Pipeline, and are not used by the game project. Likewise, the top-level references in your game project are not used by the Content Pipeline.

If that is set up correctly, then try deleting all the obj\ and bin\ directories under your gameproject and gameproject\content folders. Then rebuild everything. If there was a stale version of the importer DLL in one of those folders, the Content Pipeline might have used that instead.