<p>The located assembly's manifest definition does not match the assembly reference</p>

<p>getting this when running nunit through ncover. Any idea?</p>

This is a mismatch between assemblies: a DLL referenced from an assembly doesn't have a method signature that's expected.
Clean the solution, rebuild everything, and try again.
Also, be careful if this is a reference to something that's in the GAC; it could be that something somewhere is pointing to an incorrect version. Make sure (through the Properties of each reference) that the correct version is chosen or that Specific Version is set false.