I have only noticed the problem when visiting/living in high altitudes in Ecuador, Columbia and now Mexico. In Ecuador I lived at 3,500m for 8 months and visited the doctor several times when I was there. No health conditions found and recommendation was to move downhill. I was told that some people get used to it, some are fine on arrival, some never do. Since then have tried to stay in the range 1,500-2,000m. I have been here in Puebla, MX, for 6 months with no issues at all. However the evening / night time rains started a few weeks ago (every night) and my night time breathing issues have returned. If the change in pressure is equal to 300m for 1" change in barometric pressure it could explain things.
I am going to pack up and move this week to a place at 1,820m without the evening rains. Hopefully that helps.