SensualPoet, very interesting find.
When I was trying to figure out what I could do to alter the CSS files to get the font-sizing working on some of my ePubs. I found that if I moved the style with the font-size: 1em reference to to a class that was not being used on a <P> (paragraph) tag in the html that the whole thing seemed to work. After I found that I could do it on a few ePubs I gave up since each ePub had the HTML structure set a little differently and it meant that it was something I would have to figure out for each ePub.
I'm thinking that when you recreated the ePub using Calibre, the style sheet must have been adjusted to have the font-sizing set on a <P> and that might have caused it to stop working.
Hopefully the firmware that is coming will fix the problem completely and we can just forget it ever was.