[theducks]

1) Have you tried sorting on the ondevice column?
Yes still empty (s/b 1100 tick marks)

2) If you check the book known to be the same as the book 'in library', does it have nothing on it?
Browsing SDCard library in Calibre, selecting a title, and View shows book in Calibre's reader

3) Try doing a bulk metadata edit, change nothing, and hit OK. Do the books get marked? No change

4) Is automatic management turned on? If not, try turning it on (unless you have a reason not to).
Was OFF, Turned to Automatic (Isn't this a Sony only setting?) No change when connecting.

Spoiler:

Starting up...
Started up in 5.81200003624
Job: 1 Get device information finished
No details available.
DEBUG: 0.0 USBMS: Fetching list of books from device. oncard= None
DEBUG: 0.0 USBMS: dirs are: Q:\
DEBUG: 0.3 USBMS: count found in cache: 6, count of files in metadata: 6, need_sync: False
DEBUG: 0.3 USBMS: Finished fetching list of books from device. oncard= None
DEBUG: 0.3 USBMS: Fetching list of books from device. oncard= carda
DEBUG: 0.3 USBMS: dirs are: P:\
DEBUG: 51.7 USBMS: count found in cache: 1133, count of files in metadata: 1133, need_sync: False
DEBUG: 51.7 USBMS: Finished fetching list of books from device. oncard= carda
DEBUG: 51.7 USBMS: Fetching list of books from device. oncard= cardb
Job: 2 Get list of books on device finished
No details available.
DEBUG: 59.8 USBMS: starting sync_booklists
DEBUG: 74.0 USBMS: finished sync_booklists
Job: 3 Send metadata to device finished
No details available.
get_metadata cache: 1187 calls, 99.83% misses

NOTE: rebooted PC (because I was having trouble getting to MR only)

It now works as expected. Something is odd