Hmm... Just a guess, but in the newer version of NCM they collapse multiple returns into one, which I wish they wouldn't do. That means if you previously left several blank lines before to automatically press enter to prompts like "Destination filename [startup-config]", they don't work quite right now. I would recommend trying something like this...
copy run start
startup-config
dir
or possibly try it with multiple CRLF's instead. I usually use \n, but you could try:
copy run start${CRLF}${CRLF}${CRLF}
put some extra in just to make sure...