In these cases, where the term is made up of a combination of a simple verb (set, break, shut, log) plus a preposition (in, up, down, out, off, etc): if it's a verb, it's two words. If it's a noun, it's one word.

Another way to look at it: the verb doesn't magically grow together and apart if you use it in different tenses (past, present, future). "I am setting up" (present) is two words - therefore the "set up" in "I set up a script yesterday" and "I did not set up" also needs to be two words.

I'm no linguist, but I think it should work for most of these sorts of words where the noun is a compound word and the verb form is two words, which seems to be fairly common. ie. log in, back up, break down, work out.

Looks like the commonality is that the second word in the pair is often one of (in, out, up, down).