I'm still having this problem
with indexing. Namely that it stops at a "problem" book and won't continue. I've tried loading a few at a time but it's particular books not the amount that cause the problem.
Trouble is I haven't found a way to identify which books cause the problem so I'm left with the task of adding one book at a time and checking whether it indexes ok. I haven't got time to do that.
So I live with it - which is a shame because I actually find the search one of the most useful parts of having an ereader.