Perry Metzger talks a bit about the problems of emacs blocking starting at the 34'39" mark in his "The Editor of a Lifetime" talk[1] for the NYC Emacs Meetup. Not that his points are new, but this is just one of the first things that sprang to mind when I heard your "it works fine" claim. Here are some excerpts:

  "Threading.  This has been an irritant for me for years.  Emacs
  blocks all windows when you're doing computation in any window.
  It's an operating system, but not enough of an operating system.
  I myself will run three instances of Emacs to get around this.
  I'm slurping in my email and I can't do something at the same time
  because it's off in space slurping in my email.  It's going off and
  doing some extended computation and I can't go in another window and
  do anything else at the same time. ... If it's doing extended
  computation and a lot of file IO and talking to the network, it
  blocks you.  There's not more than one thread there."

There's also this[2] discussion of lack of threading in Emacs on the Emacs Wiki.

[1] - https://www.youtube.com/watch?v=VADudzQGvU8

[2] - http://www.emacswiki.org/emacs/NoThreading