I've deleted the css files in all the books that didn't work, and now they work fine. Interestingly though, I looked at the books that worked and they all contained a css file too. The formatting instructions must have been compatible with Kobo in those. The other thing I found was even if I wanted to simply edit the css files, when I opened them up in Notepad, they were giberish. In other words, there was no english to edit.
I expect Kobo's gonna have to fix this soon, as the average user won't be able to do this everytime they download a book. Thanks for the workaround though...keeps me happy for the time being.