I am having the same issue: after updating the cover using calibre and doing a mobi -> mobi conversion to embed the new cover, the cover shows up on the bookshelf but not on the carousel.
I have been searching all over for a solution to this, and I not found anything promising. There is a long discussion about this on the Amazon forums, where someone claims to have a "solution", though it does not seem to work for everyone:
The claim is that there is an issue with the cover's aspect ratio or it does not meet a minimum resolution. I have tried a few different resolutions but they have not worked out for me.