I have the similar effect: prove works, while dzil test not. General rule I found for myself: dzil test should be trusted.

In my case the reason for fail was caused by using File::ShareDir, and used resource in perl-code: I erased the resource from the current distribution and forget to delete it from the code. I don't know how, but prove took it from already installed package, and tests pas; meanwhile dzil test didn't do that and test failed (correct). When I uninstalled package it stared to fail under prove too.

Good luck!