I have bubbles appearing right down to the original wood after the new stain is put on. What wood cause this?

I painted a section of a wall with Kilz interior oil based primer. Since then I have put two coats of Valspar interior semi gloss paint over the same section and each time it looks as if I haven’t painted it at all. What am I doing wrong?

What color should I paint the siding on my house that has a stone front? The stone has a pink hue?