So the problem was not reference counting after all, but rather not using
another counter when adding the unknown flags to the unknown flag list (which
resulted in trying to put an element into, e.g., the 10th spot of a 1-element
list).

The speedup seems to be decent over the pure python approach, but I haven't
tested on huge systems yet.  Preliminary results suggest somewhere between 3x
and 10x speedup.

The C++ parsing routine stresses flexibility over speed. It is necessarily
slower than the versions in cpptraj and sander/pmemd since no assumptions are
made a priori regarding which flags are present and how much data is in each
flag.
~10% parsing speed boost.