I can't say with any certainty, as I have the new store format and only one place I could upload my logo, so the only thing I can think of to suggest is that eBay may be keeping old store data (because you can currently switch between them at will), and maybe the listing frame is pulling the old logo - which (if the case) you may be able to resolve by temporarily switching back to the old format, checking if the old logo image is still uploaded somewhere, and removing it if it is.
I remember that when I switched, there was some reason (can't remember what, exactly), that I uploaded my new logo when in the old store format, then switched to the new one, so if you switch, I'd upload it to the old, then switch back to the new, either way, and see if that works.
