I think the key is what you've observed about breathing.  If the nostrils
are blocked, the baby will have to slip to a shallow latch and flare the
lips at the corner of the mouth in order to breathe.  This will cause loss
of the deep latch.  Sometimes the debris is related to swallowing problems.
The baby has mild dysphagia, and is aspirating small quantities of milk
which then congeal and create debris that blocks the nasal passages.  Or,
the baby may have abnormally small nostrils.  Or the nose may be bruised
internally from the difficult delivery and the swelling hasn't yet subsided.
I would use carefully paced feeds when you comp the baby to make sure the
way the comp is delivered isn't contributing to aspiration (i.e. too fast
flow from bottle, not enough breathing breaks if using cup or syringe, etc).
See if use of baby strength saline nose drops just prior to feeding help
clear the breathing.  Never force the baby to stay deep.  Let the baby come
off as often as needed to reorganize respiration and then help him latch
again.  See if you can get the MD to really examine the nose.

Barbara Wilson-Clay BSEd, IBCLC
Austin Lactation Associates
http://www.lactnews.com

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