Sometimes you just need to wait a day until the program is able to register your games properly. Especially if you just changed your Steam profile's privacy settings to public it may take some time.
However I also had it once with one game that simply won't get registered by GoG Connect although it was listed, while my other games in the list got registered. If you really want the game to get registered I suggest to contact the GoG support right when that happens. - I guess they aren't able to find the problem just yet, since it has been some time.