In my attempts to get the Shuttle HTPC working again, I tried the official "fix the product you sold me" channels. After contacting the retailer, Shuttle and finally the wholesaler, I got the message that the fan problem I'm having is "common" and that I'd need to ship the motherboard off to Taiwan to be fixed. The fix would cost me about $15-$20 (plus shipping) and would take about 6-8 weeks.
So I played around with the system fan, PSU, some wire and some resistors. I found that a serial resistance of about 55Ω got the fan running at a good speed (not too noisy). Unfortunately, it seemed to be drawing about 300mW or so, and at that power the little 1/4W resistors let out all their magic smoke.
So I bought a 5W 56Ω resistor ($0.48), soldered it in and the HTPC is now back up and running!