The good news is that you ARE tracking coverage, but you are right that EMMA and Cobertura do not support basis paths. Path coverage is somewhat difficult to determine, but there are some technologies out there that can help out.
My company, Codign Sofware (www.codign.com) has an Eclipse plug-in that measures path and branch coverage for JUnit tests. It is available for free to open source and university students.
I also *believe* that Agitar (www.agitar.com) calculates path coverage as well, but I have never used their products personally.