After first running into the issue, I double checked line endings and tab characters in UltraEdit, using the view invisible characters bit. I should clarify, this is not Cygwin Perl, it's ActiveState Perl. I have Cygwin installed, but this is called from a Windows command prompt, not a Cygwin shell (and actually Cygwin Perl isn't even installed). The only reason I was using the Cygwin mkdir is so I didn't have to parse out the path and do repeated mkdir calls (the -p switch, if you're not familiar, creates all intermediate directories as necessary).

The original list of files and directory structures (with the not-so-innocent names) was created by someone else in Excel. I copied the data to emacs where I created the script. For the innocently named script I copied the source code, then typed the DATA lines by hand, still in emacs. So no possiblities of pasting odd characters in there. For the OS X test I copied the source code and DATA from Perlmonks into emacs.

So the short story is that I'm fairly sure that the line endings are correct for the operating system under test.

But all that being said, I would not be too surprised to learn that your suspicions are accurate. I just double checked the output of the script, and noticed that the DATA line errors occur on lines 2, 4, 6, et cetera. Yet what I would expect to be line 2 in the DATA section worked fine.

Of course now that I'm home I don't have the original script files, so I'll have to triple check line endings when I go back to work on Monday. Thanks for the input.