Hi Justin and Allan,
that error message rings some distant bells for me: maybe it's related to Perl's taint mode? Why would we be seeing a taint-related problem after changing the binary that "perl" points to? Perhaps because the file "perlcheckmate.pl" in the Perl bundle's support folder has a slightly mysterious shell-out to perl with -T turned on: line 33 of that file reads
my @lines = `perl -Tcw "$file" 2>&1`;
I'm guessing that if your path to the new perl may not be secure, or something like that --as per taint's requirements-- that message you're seeing might come flying out the other end. See "perldoc perlsec" for what triggers taint mode.
Anyway, easy to check if I'm blowing my usual volume of hot air here: just remove the taint check (ie the "T" in the line quoted) and see if the error still appears. Then you can start the hunt in earnest!
Good luck, Paul