In some quick testing, I only seem to see the ncat errors the first time I try to start pdp1control after the RasPi boots. After the first execution of pdp1control, there are things listening on ports 1040/1050 so future executions of pdp1control don't show the ncat errors.
13:46:39 ~:$ netstat -a |grep 1040
13:46:46 ~:$ netstat -a |grep 1050
13:46:53 ~:$ pdp1control start
start panel driver, either virtual or real, depends on the symlink
starting PiDP-1 hardware front panel driver
read boot config from sense switches
switches set to 1
start pidp1 in screen
start web server
Configuring PiDP-1 for boot number 1
mul-div now on
Ncat: Connection refused.
ok
Ncat: Connection refused.
start usb paper tape tool
13:46:58 ~:$ netstat -a |grep 1050
tcp6 0 0 [::]:1050 [::]:* LISTEN
13:47:00 ~:$ netstat -a |grep 1040
tcp 0 0 0.0.0.0:1040 0.0.0.0:* LISTEN
tcp 0 0 localhost:59010 localhost:1040 TIME_WAIT
tcp 0 0 localhost:59036 localhost:1040 TIME_WAIT
tcp 0 0 localhost:59020 localhost:1040 TIME_WAIT
tcp 0 0 localhost:59024 localhost:1040 TIME_WAIT
13:47:02 ~:$ pdp1control stop
Stopping PiDP-1
Terminated
13:48:27 ~:$ pdp1control start
start panel driver, either virtual or real, depends on the symlink
starting PiDP-1 hardware front panel driver
read boot config from sense switches
switches set to 1
start pidp1 in screen
start web server
Configuring PiDP-1 for boot number 1
mul-div now on
ok
start usb paper tape tool <-- no ncat errors this time
13:48:32 ~:$ netstat -a |grep 1040
tcp 0 0 0.0.0.0:1040 0.0.0.0:* LISTEN
tcp 0 0 localhost:53746 localhost:1040 TIME_WAIT
tcp 0 0 localhost:53760 localhost:1040 TIME_WAIT
tcp 0 0 localhost:53720 localhost:1040 TIME_WAIT
tcp 0 0 localhost:53732 localhost:1040 TIME_WAIT
13:48:35 ~:$ netstat -a |grep 1050
tcp6 0 0 [::]:1050 [::]:* LISTEN
tcp6 0 0 localhost:37506 localhost:1050 TIME_WAIT
tcp6 0 0 localhost:37516 localhost:1050 TIME_WAIT