Thanks for your response. Sigil points to the cover image within the content.opf file as:
<meta content="cover.jpg" name="cover" />
<item href="Images/cover.jpg" id="cover.jpg" media-type="image/jpeg" />
Within the Images folder it also shows up as cover.jpg
Where else would the mixed cases be showing up? However, if the mobi file is in no way compromized by this, then for the moment this isn't a dealbreaker. But I would like to know how to avoid it in the future.