i think it depends on the hardware... if you have a 2 channel source, lets say a CD to make it easy, and you connect that to the receiver, either digitally or analog-wise, then basically its dependant on the receiver how this is handled.
in the old days, a receiver would have just had some crossover-ish type stages in them, to automatically send subwoofer freqs to any connected subwoofers. today, how thats handled might be hardwired, or might be a user setting that can be adjusted.
personally, i expect my hardware to be "bright enough" to know to use a subwoofer if subwooferish signals exist.
so in the case above, i expect 2 channels to be whats output from winamp/hdmi/the computer/ATI, and i expect the receiver to receive it that way. then the receiver should determine how the 2 channels should be sent to the 7.1 speakers. personally, i'd only want 2.1 speakers used for whatever was stereo to begin with. but new or old, any decent receiver should be able to send the right freqs to the subwoofer.
the problem as i see it, is that the failure, or even multiple failures, could be happening anywhere along the line depending on the implementation of how things are routed.
EDIT: try playing a CD in winamp, and see if the subwoofer works. if it does, the problem may in fact be winamp for your flacs. but if it doesn't, i tend to believe the problem is with the hardware, either computer or receiver.