Converting to same format doesn't work with pdf to pdf. I have found that it works with epub to epub and I now have all my covers for epub files. But for magazines (sideloaded) and pdf files, still no covers. I am trying to figure out how to ammend meta.opf files as mentioned earlier in this thread to see if that would allow covers to show up.
I know that its not that big of deal, as I can read all of the pdf files, but now it's a challenge to get these covers to show up and its driving me nuts.
Maybe this will help tweak some neurons, at least.