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
You can change your PATH to put the Strawberry directories first. Strawberry tries to be nice by putting its directories at the end of the PATH. If you installed from the .zip file, however, it didn't change the PATH at all.
You could move /usr/bin/perl, but that's a bad idea since it breaks when cygwin tries to update what it thinks is its perl. I just had that happen to me this week and used to happen to me on my Mac until I stopped playing with the system setup and installed my own stuff completely separate.