I had a similar problem with a Makefile a long time ago. Make used whatever shell was in the user's environment rather than defaulting to a /bin/sh-like shell, and everybody used /bin/csh at the site. So I had to explicitly set $SHELL to /bin/sh in the Makefile.

Extrapolating to Perl, have you tried explicitly setting $ENV{'SHELL'}=/bin/sh before running your backticks?

In reply to Re: Specifying a shell for use with Backticks by bigmacbear
in thread Specifying a shell for use with Backticks by gaspodethewonderdog

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