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I'm going to take over this case from Owen.
When you've closed all Chrome windows, if you look on the Windows Task Manager > Details tab, are there any chrome.exe processes still listed? Chrome can sometimes stay running in the background even when all of the windows have been closed.
At any rate, this is how that option on the Window Management tab works. First window of the process only. To do what you want to do, the Trigger rule with the Frequency set to "Always" is the way to go.
Thanks!