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For the main peak (the part that is at 100% when normalised) to go from positive to negative generally requires some inversion in the signal path. Some soundcards invert, as do some amplifiers and receivers, and of course subs offer controls to invert the signal. If you haven't changed any of the equipment or settings it would be odd for the polarity to change. If by "starts with" you are referring to a part of the signal ahead of the main peak then those areas are much more susceptible to changes from the environment (positioning, treatments etc). If the measurement was a combined sub+main then altering their relative timing can also have a significant effect.
 
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