Not many people will notice the fact that you added an entirely new question to your post.

I doubt it's a problem with File::Copy. Even as far back as Perl 5.6.0 / File::Copy 2.03 / 8 years ago, copy used binmode whenever its arguments are file names (as they are in the snippet you posted).

Could you provide which version of Perl and File::Copy you are using, and could you post the first 10 lines of fc /b srcfile dstfile?