JSWolf is correct, we really should not need to do anything to get these files working on our Kobo, they work fine on other devices, I have a Kobo and my wife as a PRS-300, everything looks fine for her, but not for me.
I did some testing an it has to do with what style the font-size: is set on, if you move it off the <P> tags class it seem to work (atleast on the couple I tried) but not all books have a <SPAN> tag within all the <P> tags, and all books are going to have different style names.
Its annoying to test this all though because you can only test the file directly on the Kobo, since all the apps on my computer so the file just fine.