I have a problem with LR CC not showing RAW & associated JPG's as separate images, despite option ticked in preferences panel. ( see attached screen shoot) note this does not happen in all folders! (Note the raw images are Fuji RAF files)
I have tried various options of deselecting & restarting LR CC & visa versa etc. (What baffles me is most folders do show separate RAW & JPG's!)
If these images were imported before you checked that option, then the easiest way to bring in the JPEG images is to synchronize the folder. Or, you could import the JPEG images if that is your preference. From what you described, it would seem that the other folders were imported after you checked the option to treat JPEG's as separate images.
just as you said, sync'd the folder & the JPG's appeared