You say you know why, but don't elaborate. So, I suppose my first question is - why do you think it doesn't display in the webpage?

Without that information, my first guess is that diff isn't outputting HTML, so some of it may get lost by the webclient - but the data is still there. So I'd suggest something like:

  print "<pre>", `$DIFF ...`, "</pre>";
[download]

The diff output is pre-formatted anyway. If you want to spice this up, you'll have to parse the output and deal with that yourself - but that's stage 4 or 5 of this process, I bet ;-)

Minor nit: I think you mean if(-e $setuidtoday && -e $setuidyest). The -e operator doesn't go across the && the way you seem to think it does. Since $setuidyest is always true, the way you have it, that's a no-op. You probably want to test its existance.