That could be the problem: the main DualISO algorithm is the only part of the processing engine which has to run on a single core (preview mode is multithreaded, but quality is worse). So just for the little time of aligning, just one core will have 100% usage (before and after that, all cores are used).
Sry... DualISO is one of the features I barely use, so I forgot about its special realization.