I currently use Strawberry Perl as my primary Perl distribution. However, I have some applications that make Perl calls through cygwin. These generally fail because they are
I don't have my cygwin machine nearby so I can't test this, but perhaps you can front-end the perl command with a script: go to /bin under cygwin and move the perl.exe there to something else like perl-org.exe, then set up a shell script that execs your other perl with the same arguments.
I have two scripts that I use to modify the first line of Perl scripts to whichever Perl is first in my path: rightperl hardcodes to the Perl that is first in my $PATH now, envperl will change the line to #!/usr/bin/env perl so the Perl to use is only picked at the time the script is invoked. Works really well under Cygwin (and from a Unix shell in general).