Are these modules per-chance pulled in with either a dynamic eval (eval "use MyModule") or some other such thing? I am not sure, but that might have an effect on things. You could also try explicitly use-ing those modules in your test suite itself (if you are not already that is), which might make Devel::Cover take notice of them and help you determine if that is the issue.

You should try isolating the problem and sending the author a note with your example code. I know he also hangs out on the perl-qa mailing list.