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
This is probably not a preferred solution, but you should be able to modify the #! line:
#!/cygdrive/c/strawberry/perl/bin/perl5.10.0
I always refer to an explicit location and installation of perl, rather than relying on what is in /usr/bin.