Are you forgetting to bitshift 8 bits to the right? This certainly works under my modperl.

$ cat exit.pl
#!/usr/bin/perl
print "Exiting with $ARGV[0]\n";
warn "Sending to STDERR\n";
exit $ARGV[0];

$ cat test.pl
#!/usr/bin/perl
my $output = qx! /home/www/modperl/exit.pl 42 2>&1 !;  # capture STDOU
+T + STDERR with 2>&1
my $exit_code = $? >> 8;
print "Content-Type: text/html\n\nExit: $exit_code ($?)\n$output\n";

# OUTPUT -> Exit: 42 (10752) Sending to STDERR Exiting with 42
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Note: If you have installed a signal handler for SIGCHLD, the value of $? will usually be wrong outside that handler.