As the code for the package: org.jboss.jbossts.xts.servicetests.* exists in "src/main", i.e. ./XTS/localjunit/xtstest/src/org/jboss/jbossts/xts/servicetests it is being instrumented and its numbers are therefore affecting coverage.
Interestingly the numbers are actually showing zero percent rather than 100% for these packages, so the first thing to investigate is why does this code exist and are we actually using it to test. After that we should exclude this package in the root /pom.xml in the emma instrument goal similar to the orb generated source.