All right, please find a revised patch attached that does not stop the CPU fan.
Turns out that the original patch malfunctioned on both v1.1 and v2 of the board if the it87 driver was not loaded. That driver fixed the settings, which added to my confusion. It also explains why it seemed to work for me at first, but then did not when rebooting (I was booting a different filesystem that did not load the it87 module on startup).
Anyway, I'd be grateful for some testing of the attached. It does the right thing on v1.1 and v2 of the board based on my testing. It does not set the diode zero adjust temperature right yet for v2 of the board (it should be 0xfe instead of 0xec). That could be done by adding a detection for the revision of the IT8716F chip (v2 seems to have rev3, v1.1 has rev0), but I don't have time to add that right now. It's not that important I think - but if someone wants to contribute that change, please feel free. There are a few other registers that should be slightly different between v1.1 and v2 but nothing very crucial it seems.
Thanks, Ward.