(this is based on Kindle Touch, my PW won't be delivered until tomorrow, but they should be very similar)
The images you see don't come directly from the book file. They're to be found in /system/thumbnails. They're all 157 pixels wide (this might be more like 200 pixels on KPW because of the greater resolution). The height is proportional to the original cover image. I believe Kindle generates these on the fly from cover images found in the book file (or application).
But at least on Fire, cover images have to be of some magic dimensions before the thumbnails will generate and display. When you send things to personal document service metadata (and covers presumably) get 'sanitized' so these will always work. But when sideloaded, this sanitization doesn' t happen. So I'd check the cover dimensions calibre is using and compare ones that work with those that don't, and see if a pattern emerges (for example, if larger resolution images always fail). Or you might search the Fire forum here for the thread discussing the similar issue (I've just read about it, but haven't dealt with it directly myself).