jmvcRoot should be set to url of JMVC's root folder.
This is used to calculate JMVC style paths (paths that begin with //). This is the prefered method of referencing pages if you want to test on the filesystem and test on the server.
This is usually set in the global config file in funcunit/settings.js like:
FuncUnit = {jmvcRoot: "http://localhost/script/" }