I was working a different issue and found that I can reproduce your symptoms.

Send/Receive Define Groups (Ctrl-Alt-s).
{Select "All Accounts"} -> Edit

{Select an account}
(o) Use the custom behavior defined below

{In the Folder Options pane}

If a folder is not checked, then the Outlook initial sync and Sync All (F9) do not pull in new mail. But if I switch to that folder, or open it in a New Window, it does a sync on that folder.