As I understand it, there are at least two modes of sleep on these machines: deep sleep and "light" sleep. in "light" sleep, the fans don't go off, whereas in deep sleep, everything goes silent. I don't know why this is, I just know that it... is.
I have found this to be a problem under OS 9 when I have a USB card installed. Presumably because OS 9 doesn't understand USB 2.0, it complains that the card is preventing the computer from sleeping properly. The same computer with the same USB card sleeps just fine under OS X 10.4 and up, so it's probably a software issue. Since USB 2.0 drivers don't exist for OS 9 (yet?), this is a problem with no solution, other than running OS X instead for full sleep capability.
So perhaps this is what you discovered.
Apparently that SCSI card isn't supported by the computer somehow. Do you know exactly what make/model of card? Perhaps you can find one which is more fully compatible (perhaps an Apple-OEM card?)
It could be, or it could simply be that the fan was defective and died early.
I hope this helps...
c