Very good point.  I actually considered that, though, because I had had exactly such a problem at work about 3 or 4 days ago (a Linux tarball was unzipped on Windows, then put back together, and none of the scripts in it behaved correctly -- turned out they had all been converted to [dos] format).  So I had already done a dos2unix on "hello.pl", with no change in the results.

As far as running strace, I hadn't think of that, and it's a very good suggestion too.  Unfortunately, running it on the simple hello.pl program doesn't yield significant differences between the two.  Most of the differences are memory locations, with the exception of a complaint about some invalid ioctl in /dev/urandom (but that happens with the strace on the version of hello in /var/www/html, which is the working one).  Otherwise, they both indicate the same values for what was (supposedly) being output.