Answering my own question in hopes it can help somebody.
At time of writing, there is a known bug with Cobertura throwing a ClassNotFoundException in certain circumstances. See the following issue tracker page: https://github.com/cobertura/cobertura/issues/74#issuecomment-41383903
For the time being, I've gone with EclEmma Eclipse plugin for EMMA for my test code coverage, and got nice, pretty results the way I wanted.