Hi, and thanks for your post.
When you click "Configure" in Multi Script, it'll search your network to give you a list of available servers. This works by running a query that partly relies on the SQL Browser service running on the servers, and could explain why some weren't listed and you had to add them manually (i.e. they couldn't be detected).
Once you have the ones you want in the list, you then click "Add" to move the ones you want to actually work with over to the right. You can add them to the default list, or create a new list of servers by clicking "New" at the top, and entering a name - for instance, "Geri's list".
Once you OK that, then you can select your list in the main SQL Multi Script screen and you'll just be working with the servers you want.
Regarding your original query of removing servers from the selection screen, this isn't possible unfortunately, as a search is performed when you go into that screen. The idea here is to present you a list of as many servers as possible to minimise the need to add them manually. The lists enable you to then work with just the ones you want, so the extra ones aren't in the way.
Hope that makes sense.