Well first of all check that the connector is actually plugged in on the backplane!
If it is then the quick way to find out if it's the fan or the board is to plug another fan in and see if that works, if you don't have another one to hand then you can use the front fan, the connector is the same and they're not that hard to remove and swap but you might have to get a bit creative as to where you put everything to power it up!
The other option is get a multimeter on the outputs to see if anything actually coming from the connector but that's tricky as there's not really room to do it without making a dummy connector lead and trailing that out past the CPU...
EDIT - just realised I'm talking about the CPU cage fans and you might be meaning the booster fan in the CPU heastink?
If it's the booster fan then that's harder to test without just replacing it as you can't really subsitite another or get to the connector while the machine is running. It would be worth popping the heatsink off though and making sure the connectors are not damaged.
