First off, the root issue has more or less been reported here: Print Setup[Restore] in Filemaker Go. But the issue has not been clearly defined yet, which is why I am starting a new discussion.
In FileMaker Go, a Print Setup step will commit the record in all windows. I consider his a bug for two reasons: 1) FileMaker Pro doesn't act this way 2) actions performed on one window aren't supposed to affect other windows, generally speaking.
In testing this issue, I've also found a related issue: If the second (inactive) window has an OnRecordCommit trigger script, and that script has a Refresh step in it, then FileMaker Go will hang.
I've attached a sample file that demonstrates these issue, as simply as I could think to do it. The sample file comes with instructions.