I have noticed that a few of my sideloaded books will have covers initially, then sometimes disappear and be replaced with the generic text (title) of the book. After rebooting, they show up again...almost like it's a refresh issue or something.
Also, if you use Sigil to modify your ePub, I noticed the file structure of the ePub changes dramatically. There are a couple of ways to organize the HTML inside the ePub I know...
How do I know? unZip your ePub made from Calibre to a folder.
Modify the original ePub with Sigil, and then unZip that ePub to another directory and compare the contents.
At least in the one book I was working on I noticed this. I was breaking my book into chapters with Sigil that were absent in the original ePub. If you wish to retain the original structure for whatever reason, Sigil and Calibre appear to not be identical in ePub creations.