Waht program did you use to make the charts? What format are they saved in? Are they "exploded"?
My guess is that they are not all at exactly the same coordinates in the creation program, and that your crop options on import are set to something like media that uses the whole file, not just the artwork in the chart.
It's also possible the frames into which you've placed them are not the same size and shape...
Okay, the pies themselves are all the same size, but I imagine it's unlikely the labels around them are all identically sized and placed. Depending on how the bounding of each chart group is being determined, it may be that some pies are landing at differing coordinates in relation to "center." You might be better off finding a reference point that is more likely to be constant across all the charts in terms of proximity to the pie...one of the corners perhaps.
It's certainly not out of the question that achieving agreeable alignment simply by way of consistent method may be impossible. Sometimes you just have to give in, set some guides, and drag by eye. Might get you done quicker than agonizing over elusive inconsistencies.