I've run into this problem too, though I don't have an appropriate file on me to test out. Two options come to mind, though - I bet you can probably fix it by checking the tickybox for "Use cover from source file" on the main conversion page.

If that doesn't work, I guess the slightly more complicated method could be to remove the cover image from your .epub file, upload the .epub into Calibre, then add the cover image separately. If you then convert to another file format (say, .epub to .mobi), that cover image will be added into the new file; maybe you can then convert back to .epub? I'm not sure how much formatting might be lost in the backwards-conversion, but if you're desperate that should work well enough.