Brandon spake verily:

 I have solved our problem with triple-quotes.

 The problem is that Emacs expects PyFlakes to only output error
 messages, but on a syntax error, PyFlakes prints out an error message,
 then the *entire* contents of the module that it cannot import, and
 *finally* a line that contains a number of spaces equal to the offset
 into the file of the syntax error (in the case of my real-world file,
 the triple-quote was 3,896 characters into the file, so PyFlake's line 
 of spaces was that long as well).  The offending code is in the
 "pyflakes" command-line program and looks like this:

    print >> sys.stderr, 'could not compile %r:%d:' % (filename, lineno)
    print >> sys.stderr, line
    print >> sys.stderr, " " * (offset-2), "^"

 By removing or commenting out those last two lines, so that PyFlakes 
 only outputs its error message, you will stop flooding the Emacs
 regular-expression engine with data.  It's actually the long line of
 spaces that causes the problem, and it's one regular expression that's
 really sensitive to it (this is from the Emacs 22 flymake.el):

     ;; ant/javac
     (" *\\(\\[javac\\] *\\)?\\(\\([a-zA-Z]:\\)?[^:(\t\n]+\\)\:\\([0-9]+\\)\:[ \t\n]*\\(.+\\)"
      2 4 nil 5))

 For some reason (I'm not an RE engine guru), something about the way
 it's matching spaces takes exponential time when given several thousand
 spaces.  Go figure.  Anyway, I see no point in throwing anything but 
 error messages at Flymake, so I comment out both the printing of the
 module and the spaces from PyFlakes.

And sure nuff, that solves it. Brandon gets a well-deserved $500.00.