If you view both folders in the outline mode, and enable the appropriate columns, can you set the target then? If so, does the target show up for your problem folder after that?
That should make no difference. What does appear in the footer bar? Could you be in scriptwriting mode? Also, note that the target icon is only available if you view a single text document - if you are in scrivenings mode, the target for all the documents in that mode will be shown, but the “set target” button won’t be visible since the target shown is for combined documents. So be sure to switch the folder to single-text mode (turn off the corkboard, outliner and scrivenings) to set the target.