A few problems here. First, a longer barrel does not help mechanical accuracy (it does not necessarily harm it either). Second, the M17S isn't a precision rifle.
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It seems like the overall length of a standard rifle is an extension of the barrel allowing you better accuracy (it seems easier to steady).
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This is the rear-heavy balance issue I referred to.
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With the bullpup it seems like a small error at my hand or shoulder will equal a much bigger variance at the target
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This goes along with the prior point, but it is more likely a difference in the bipod position. The further the bipod is from your shoulder, the less POA movement you'll see when the rear of the gun moves (ie at your shoulder).