The problem is that $kid is the pid of the shell you launched (since you provided a shell command), and it exits as soon as it launches java. You could avoid the shell.

use IPC::Open3 qw( open3 );

{
   open(local *CHILD_STDIN,  '<', '/dev/null') or die;
   open(local *CHILD_STDERR, '>', '/dev/null') or die;
   local *FROM_CHILD;
   my $kid = open3('<CHILD_STDIN', \*FROM_CHILD, '>CHILD_STDERR',
      'java', 'JavaApp'
   );
   ...
}
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Higher-level solutions possible using IPC::Run3 and IPC::Run.