I'm going to guess that the indexes are corrupting. Like I had mentioned earlier, MySQL suggests 4 characters as the minimum for the ft_min_word_length variable. They say 3 can be unstable. You said that you had to kill the process of it rebuilding the index, so I think you're full text index is out of whack currently.
The posts table is written to much less often than it was in previous versions as we store more things in the topics table instead, so my first guess would be the indexes corrupting and not the table itself.
