You have to start script either interactively (which opens a virtual terminal, or something), and then start your command.

Or you use the alternate syntax script -c COMMAND log_file, which means you'll have a mess with quoting, unless you use the LIST form of system:

my $command = qq{perl -MCPAN -e 'install q/Bundle::Snapshot_2007_07_23
+_00/'};
system('script', '-c', $command, '/cygdrive/c/cpan.log');
[download]

(not tested)