Assume you have two files with coverage from two different test suites. Let it be manual.xml and auto.xml.

Next commands, then, generate two reports which are not consistent.

Merge:
$ files="auto.xml manual.xml"
$ jdk/bin/java -jar jcov/lib/jcov.jar Merger -o complete.xml $files

Generate two reports:
$ jdk/bin/java -jar jcov/lib/jcov.jar RepGen -nomethod -noline -nobranch -o per_suite_report $files
$ jdk/bin/java -jar jcov/lib/jcov.jar RepGen -nomethod -noline -nobranch -o report complete.xml

Block count in the rightmost column in the "report" report is different than block count in the "per_suite_report".
It looks like there are no inner classes in the report.