Are you waiting for the Job Wheel to stop spinning (and say 0)?
Calibre transfers the book, then it updates metadata.calibre ON THE DEVICE.
When you connect again, that is the first file retrieved (after device identification). If that file does not exist (or corrupt) Calibre scans your device... <time passes> then INITIAL status is updated,
(Guess from observed behavior) next the changed items status is processed <more time> NB Items that were changed in Calibre after transfer will initially show as Not on device, and will update after the changed scan completes.