Something is trying to do something with those command windows that it is opening.
You need to try to figure out what is using those command windows at start up and then maybe reinstall that program or disable it from starting.
Odd behavior like that sometimes might indicate you have a virus. Perhaps you might want run your virus scanner and do a full scan ?
I see you've apparently asked somewhere?:
What is the location of that External Hard Drive ? Is it attached to your router?
Right click one of those 'shortcuts' and select 'Target' and copy & paste that here.