This looks as if it's made to run as a CGI, so the first thing I'd do is look in the web server's error log.

I'd also suggest that every open be followed with some variation of or die $! (I see one does have that, but others don't).

Check that the files you're expecting to be there really are there (if you die on open failure, that should make this problem obvious).

Note that Perl has a built-in chmod, so you don't have to use backticks. (And backticks in void context is frowned upon. Use system for that.)