I'm starting to notice some patterns in this.  It may have to do with the version of Bitcoin-Qt that produces the blk*.dat files.  It's very possible that there are artifacts in the blk*.dat files that I don't handle gracefully. 

So where did your bootstrap file come from?  Do you know the version that created it? 

On the other hand, I'd like to move away from reading the blk*.dat files entirely, and just request it as a regular blockchain download via P2P (via localhost).  This would solve a lot of problems and should make the version of Bitcoin-Qt irrelevant, in addition to allowing remote Bitcoin-Qt instances.  In fact, I wanted to do this for 0.90-beta, but the change was too dramatic, and decided to keep it simple for now.  But now that this version is stabilizing, it may make sense to do that, especially if it wipes out these kinds of bugs, which may be elusive and difficult to debug (basically allow bitcoin-qt to read its own blk*.dat files properly, and pass us the data in standardized network messages).