Clamping inductive kickback of PWM fans?

02660:
I usually use them for the low voltage drop, but in this case it was just what I had in the parts bin.

Well, that's as good a reason as any.

02660:
That is one reason I am asking is it the correct type to be using? My understanding is a faster diode will perform better in this application?

I don't think so. As best I know, distinctions between diode "speed" refer not to how fast they turn on, as all do so very quickly, but as to how fast they turn off, due to the persistence of carriers in the junction region.

02660:
The better spot for the diodes would be at the driver?

Absolutely. As in the article dlloyd cites, it's not just the motor, but the cabling, and you even have to account for the cabling to the power supply, so to protect the switching device, you have to have a "stiff" local return (capacitor) for the kickback diode to work to since it is connected not to ground but to the positive rail, otherwise the spike appears on the supply rails as well, which is what I suggested you test for to start with.