My best guess at what is happening is that the coverage for the symlinks is getting merged into one report (this is a feature), but that the symlinks are still getting reported on (this would be a bug). Could that be what is happening here?
Are you able to put together a test case? If so, please send it to RT (I don't really follow perlmonks) and I'll have a look at it. If not, just a bug report there would be better than nothing.
For future reference, the best place to report stuff like this is probably the perl-qa mailing list. Not that I have any problem with people discussing Devel::Cover wherever they want to - quite the opposite in fact - but when we get to bugs perl-qa or RT is probably needed.
I don't suppose there's any chance of getting your parallel modifications into the main distribution?