Perhaps try invoking Devel::Cover a different way. I use the following commands and I've never seen it test anything outside of the directory in which I was working.

cover -delete
HARNESS_PERL_SWITCHES=-MDevel::Cover perl ./Build test
cover
[download]

Actually, what I really do is use a bash script:

#!/bin/bash
if [ -f Build.PL ]; then
    makecommand="perl ./Build"
elif [ -f Makefile.PL ]; then
    makecommand=make
else
    echo Cannot generate coverage information from this directory!
    exit 1
fi
cover -delete; HARNESS_PERL_SWITCHES=-MDevel::Cover $makecommand test;
+ cover
[download]

I wish I could help more, but I'm currently at the limit of my experience on this issue.

Good luck.