I know we worked to improve this in build 315, but apparently there's still some issues. Is there a way you could save and email a copy of your MRF saved from NEWT and email it to support@komodolabs.com? You can delete all other devices in it except for the servers and you can Zip it if you'd like. We'll take a look at it and see about getting this fixed ASAP, hopefully within a week after receiving the MRF.
If the server can be pinged or it responds to NetBIOS requests ("nbtstat -a [hostname or IP]" in a DOS prompt, NEWT should scan it ok and not give you that error. Can you check that with one of the servers you're having trouble with?
As a workaround to get a successful scan until we can improve this further, you can disable "Require Windows-style responds to scan" under Preferences.