Either of these will work:

1. Use a synchronous system and the start command. This will synchronously run a copy of cmd.exe to run the start command, and it starts the program asynchronously.

   As cmd.exe returns immediately and the synchronous system gathers its exit code, it avoids the accumulation of zombies and the WaitForMultipleObjects() problem:

   for ( 1 .. 100 ) {
       print "spawning job $_";
       system 'start \\Windows\\system32\\notepad.exe';
       my $wid = WaitWindow( 'Notepad', 1 );
       SetForegroundWindow( $wid );
       SendKeys( '%{F4}' );
   }
   [download]

2. Use the asynchronous system and obtain the pid of the started instance from the returned value.

   Use waitpid to gather the exit code thus avoiding the accumulation of the zombies:

   for ( 1 .. 100 ) {
       print "spawning job $_";
       my $pid = system 1, '/Windows/system32/notepad.exe';
       my $wid = WaitWindow( 'Notepad', 1 );
       SetForegroundWindow( $wid );
       SendKeys( '%{F4}' );
       waitpid $pid, 1;
   }
   [download]

Finally, 'Simpo PDF to Text' has a 'batch mode' which would be possible -- if awkward -- to drive programmically, but it might be substantially more efficient.

I guess you've already looked at command line driven alternatives?