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Well, technically you're doing something wrong, because you're not connecting the Pod in stereo.
It could be that (part of) the reason why it sounds different is that the stereo-effects are now lost (things like reverb, delay, chorus etc just have a way of sounding better in stereo).
Other than that, you're going through extra preamps and AD/DA converters when you run through the PC. That can impact tone aswell.
Can't you connect the Pod directly with USB? That way you get the original digital signal from the processor, and skip the whole DA/AD stage when going to an analog output and then an analog line-in.
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