Would like to chime in I have this exact same issue, and I've also had it happen in a different place (Broken Wing - Zeffo). I've checked three different guides and spent all Friday evening crawling over everything.
I think the issue for me is that in BOTH of these areas, I got both secrets the first time I came to Zeffo, then didn't come back until after the entire storyline finished. Both areas are stuck at missing 1 secret for each, I'm 100% sure I've been through each secret area multiple times.
