I have no experience with high altitude baking but I have definitely had the sinking cupcake issue before. I don't know what caused it but it only happened once or twice and hasnt happened in a really long time. I did google the altitude thing really quickly and found this:
Adjustment for 5000 feet:
Reduce baking powder: for each teaspoon, decrease 1/8 to 1/4 teaspoon.
Reduce sugar: for each cup, decrease 0 to 2 tablespoons.
Increase liquid: for each cup, add 2 to 4 tablespoons.
Increase oven temperature by 25 degrees F.
Hope that helps!