The remote tests in JTS were developed to be run manually with specific interceptor options mentioned on the command line. Although they are now junit tests it doesn't seem that all of the options are being used, or perhaps the server side component isn't being covered by emma, because interceptor classes that should be called aren't mentioned in the report.
These tests are actually multi-jvm i.e. qa style tests, not unit tests. So the problem is actually in two steps: Move the tests to the qa suite, then enable emma on the qa runs.