I had that problem (publisher font showing as helvetica) when I first started trying to embed my own fonts with Calibre. Turns out I under the "Filter Style Information" tab on the "Look and Feel" section of the conversion screen I also had the box checked to "completely remove fonts". When I unchecked that and tried the conversion again, it worked perfectly. (Thanks to booklover6 for pointing me in the right direction on this!)
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