At a guess, it is getting eaten because it is a Windows-specific construct in a module which doesn't fully compensate for the Windows approach to current working directory.
In my early days of Perl on Windows, I found a lot of the modules didn't quite handle the Windows-unique stuff as gracefully as I'd like, and so I wound up writing modules for myself to compensate.
Also, you look to be doing things in a more Linux-y environment that seem to be Windows-esque. Are you running under Cygwin?
I seem to recall some special kinds of weirdness can happen when running under Cygwin which exceed even the Windows/Linux weirdness matrix.
Been a long time since I've used those environments, and the modules I rolled for myself over a decade ago still serve me well, so I haven't revisited these kinds of issues in a very long time.
Hope someone gives you better insight, but I can't tell from you snippet above exactly how to reproduce your problem, much less resolve it.
Here's hoping a more familiarized Monk recognizes what you're doing.
If you'd like, I suppose I could post what I use to get and set current working directory, but I really don't know if it's all that robust -- or even as portable as I'd like.
Let's first see what others come up with.
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