At this point I'm really just guessing: I don't know enough about the binary formatter to give you an accurate diagnosis.
In .NET, assemblies can be referenced either by assembly name (as in the error message you posted above), or by filename. Judging from this message, the formatter must be looking by assembly name.
The content pipeline build runs in a temporary worker appdomain. To get an assembly loaded into that domain, you add it as a reference to your content project. We will load the assembly either by assembly name or by filename, depending on whatever format the reference specifies.
Obviously, your assembly is being loaded into this appdomain - otherwise none of your code from it could be running at all! But it may be getting loaded using a different name to what the formatter is looking for, so it cannot later resolve the assembly reference.
It's possible you might be able to fix this by manually loading the right assembly yourself before calling the formatter. Alternatively it might help if you gave your assembly a full strong name (at the moment you don't have the public key token filled in).
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