The value of $? is associated with the last successful waitpid call. In your case things are complicated because you are calling waitpid in two places: your main program and the SIGCHLD handler. I wouldn't be surprised if the SIGCHLD handler is causing $? to get clobbered (with respect to the waitpid call in your main program.)

I would get rid of the SIGCHLD handler, and structure your code to look something like this:

my $script_pid = fork();
...launch script process...

my $abort_pid = fork();
...launch abort button process..,

my $pid = wait; # see who finishes first
my $st = $?; # save status
if ($pid == $script_pid) {
  # script finished
  kill 9, $abort_pid;
} else { # assume $pid == $abort_pid, or check it
  # abort button finished
  kill 9, $script_pid;
}
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