Interesting that I haven't seen the bug you describe myself (maybe it's OS-specific or only manifests for projects in paths with capital letters, etc.). This change looks fine, but 2 comments:

1. Is includes still needed, or is straightforward equality checking sufficient?
2. I assume require.resolve is somewhat expensive, so can you pull it out into a variable to avoid computing it for each check? (if it does its own internal caching then nevermind)

I can merge and push a new release tomorrow.