Nope not true, epubs have standards that means covers are formated a certain way. Some covers can be a little larger but eseentially they are the same. This is not true of mobi or lit where the format is different and yes you have to make sure of those settings you mention. What ever calibre does it screws things up on the touch. if the covers were not correct, they would not show up when you do a factory reset. You would still have blank covers. But the fact that once the touch is reset and that calbre has no contact with your touch tells me that something is wrong with calibre.
Not trying to be argumentative but I'm not sure why you feel my statement is not true. When I first started using calibre with a KT I had multiple instances where the book loaded without a cover image. I read posts in the calibre forum regarding this issue, where multiple people stated you need to do convert the book before you download it, in order to insure you get the cover image, along with the book.
If the book is already in an epub format thats ok, but you will still need to do an epub to epub conversion. I have downloaded at least a hundred books since and I have yet to have another book download without a cover.
Have you tried doing a conversion prior to downloading? You may have a separate issue but while I was one of those people questioning whether calibre was a problem earlier, I've made the adjustments I referred to earlier and I have not experienced any more problems and I use calibre on a daily basis.