Ok, then try this (epub to epub conversion): select one of the problem books in calibre, click on the arrow next to the Convert Books icon, select "Bulk Convert". Click on "epub output" (bottom left of screen) and check off "no SVG cover". Click "ok". If you get the pop-up asking if you want to re-convert, select "yes".
If that doesn't work, I'm all out of ideas...
for the cover size, I usually pick approx. 300 X 500 which is what the Amazon covers usually are when I edit my metadata using the "edit metadata" --> download metadata (or download covers) in the edit metadata pop-up.