Why might I have trouble making butter from Crème Fraîche?
If you were using supermarket cream, the reason would be very clear: it is not only pasteurized, but also homogenized. This means that it has been mechanically emulsified to prevent the butter from separating. 

I don't know if the cream for creme fraiche is homogenized too before creme fraiche is made, but with your result, I'd suspect homogenization too. It won't show up on the label as an ingredient, as it is done by forcing the cream through microfilters.