Ok, the CPU fan problem was a dumb error due to plugging my CPU fan into the OPT_FAN1 slot and my Case fan into the CPU fan slot.
Tried different combinations of plugging the fans into the PSU (it's a Thermaltake Toughpower XT so the PSU is modular. Side fan is still the only one that turns on. The BIOS doesn't detect any fans in the mobo besides the CPU fan (I have the 2, one in OPT_FAN1 and one in CHAS_FAN1.
The fans are pretty much http://www.thermaltakeusa.com/Product.aspx?C=1164&ID=1721.
(Shouldn't need to be plugged into the CPU, except as an RPM monitor).