Rodney,

After converting the mbox file to Maildir and adding it to my mailstore,
I cannot reproduce the loop.  (The versions of notmuch and emacs I used
are close to the ones you have, but not an exact match, so it may be
something subtle about those versions.  I can investigate
more carefully if it seems like this is the case.)

If you do:
M-x set-variable RET debug-on-quit RET t RET
then trigger the loop and press C-g, you should get a buffer showing a
backtrace of the lisp stack.  What does that say?

Thanks,

-- 
Aaron Ecay