@blaenk - Try turning off WiFi when transferring books via Calibre:
- Turn off WiFi on your Kindle
- Send to Kindle via Calibre
- Open Kindle; cover used by Calibre should appear
- Wait, I dunno, 5 minutes or so? Or until book is finished indexing, or whatever processes Kindles goes through with new books? Just give it a few minutes.
- Turn on WiFi and see if cover is replaced
I'm working from fuzzy memory of when I was experimenting with sideloading books via Calibre (which I no longer do). I won't swear my fuzzy memory is accurate, but I seem to recall that when WiFi is off, you get the Calibre cover, and once Kindle finishes processing the book, it won't look for the cover from Amazon's servers. But again, this was a while ago and my memory is fuzzy.