However, in my case, I want the script to send output to the console, read some input, fork a process, send more output to the (same) console, fork another process, send more output, fork another process, send more output, then quit. As I understand $con->Free(), I think it permanently detaches from the console. Sorry for being unclear.
OK, using the Win32::Process with DETACHED_PROCESS when starting the app seems to have cleared up my problem. Honestly, my code in total looks like garbage, but it runs. Thank you Perl ;)