FWIW root and telnet are a bad mix. You should be using SSH in this day and age.

Anyway Telnet is a funny protocol that involves a Network Virtual Terminal, or in short there is a lot of hidden complexity. As you may have guessed I don't use Telnet for anything more serious than talking to SMTP, HTTP, or POP servers off the command line - but I have two suggestions. Fire up the command with nohup ie cmd("nohup ./some_command &") and see if that fixes the problem. If that fails there is an example in the Net::Telnet docs of how to fork a new connection so perhaps just fork a new conn and run your long running command in its own shell.