Don't see how it could be a Kindle app issue. I'm using the same Kindle version with both Calibre 0.8.20 MOBI files and with Calibre later-version MOBI files.
With 0.8.20 (and all previous versions) files, Kindle automatically includes the MOBI files in its library. With later-version Calibre MOBI files, Kindle ignores them.
Must be that something in the Calibre MOBI file structure that's changed.