include script B as a sub and fork - quick and dirty...

# print cgi response as usual, then...

my $pid;

if ($pid = fork) {
  # display run, so exit
  exit(0);
}
elsif (defined $pid) {
  # run script b function if $run_script_b true...
  if ($run_script_b) {
    script_B();
  }
}
else {
  # raise an error coz the fork failed
  ...
}
[download]

Works for me. My script starts an FTP install that can take up to half an hour to run, depending on network connection.

cLive ;-)