is it not a good idea to keep and run a few of these tools occasionally then?
No, it's not a good idea to keep these programs on your machine. They become outdated and don't do their intended job properly. Also in many instances they have quarantine files that contain the bad files they have found. Best to remove them off your machine.
That doesn't mean you can't run them again if you want to. Just download the latest version.
I have just noticed that I get a black command box when the pc initially starts.
Yes I get that on my machine for a few seconds before it goes to "Windows is starting".
Do you think this is something different on your machine? That is, it didn't happen before?