I just opened an ID file with alternate layouts in ID CC. All the pages were there but, they were not layed out in the pages panel as alternate layouts; there was just one long list.
I selected a page and chose, "Create Alternate Layout", and the alternate columns in the Pages panel appeared. Command-Z deleted the last layout group just created.
Just thought you would like to know.
BTW, I wish it were possible to swap one page of an alternate layout with the first page of that alternate layout; unfortunately, that does not seem possible. It seems the first page must always remain the first page. This is my wish for the next update.
Did you try opeing the Pages panel flyout menu and choosing View Pages > By alternate Layout?