Well, I have the same issue with my MDD Powermac. I have a macally 4port USB card in one of my PCI slots and the sleep issue is the same. Put it to sleep, the fans still run and it won't wake up. I have to do a hard restart if I get into this situation.
If you head over to xlr8yourmac.com, they have well documented this issue with MDD Powermacs (and other G4 powermacs). PCI card makers and the chipset makers say it's Apple's problem, Apple insists it's their problem. Then there's us, stuck in the middle of this war and neither side is going to solve the problem.
So my best advice and only work around (that I found) is really annoying. The card must not have anything plugged into it that doesn't have it's own power source (i.e. - a printer is ok, but an iPod is not). That goes for the cord as well. If I leave my iPod USB sync cord in the card when I put it to sleep, I have a hard restart on my hands. Printers and scanners seem to be ok, but that's about it (again, in my experience). If I remember to take out all of my unpowered cords, then the Powermac sleeps like a baby. If I don't, it's a dead duck with spinning fans.
Let me know it that helped at all. I probably went through 3 or 4 months of this hell until I figured out a solution.