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.

In reply to Re^3: Limited Coverage by molecules
in thread Limited Coverage by Herkum

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