Change your script to:
copy running-config startup-config
startup-config
Oh wait, is it really asking to confirm the Source Filename? I've only seen it confirm the Destination Filename. Like this:
#copy running-config startup-config
Destination filename [startup-config]?
Either way, answer each question explicitly, don't try and put in enters or linefeeds. Solarwinds broke this ability a few versions back and now you have to be more explicit... They now collapse multiple consecutive returns into a single one.
YA plea to Solarwinds to interpret multiple returns in a script as just that!! Multiple returns!!! Makes our life much easier...