I ran into this problem as well. Seems like something funky going on with iBooks 3. Anyways, I had to tweak my read-aloud clip starts in the smil. Where the word was not highlighting, I added a few milliseconds to the timing until the word started highlighting again. Not the most ideal solution, and not sure what exactly causes it because 90% of the words were just fine, but it seemed to fix the problem. Note prior to the problem happening, I had all my clip start timings = clip end timings for the previous word, so there were no gaps.