Well, first of all, that first chord is a Bm add9. The minor 3rd makes it a minor chord. If it was B major it would have a D# instead of just a D.

It sounds like you're talking about intervals with all that augmented/perfect stuff. But that doesn't really have anything to do with whether or not a chord is major or minor.

If you have a major triad, 1,3,5, you flat the 3rd to make it minor.

As for the scales, the minor scale is built upon the 6th note of the major scale. If you go to the 6th note of the scale and count up the 1st, 3rd, and 5th notes from the sixth you will have a minor triad. This is just another way of flatting the 3rd of a major triad . . . or just another way of thinking about it anyway.