Were both the stain/sealer and the poly compatible? Same brand or not, there are oil based and water based poly's, and they don't play well together. The other thing is that Minwax poly's are garbage. They are hard to work with and leave a poor finish quality behind, so regardless of compatibility with the stain, you're going to get a rough finish, and yes, Minwax poly's dry to a milky haze that gets worse the more coats you put on. Your next project, try McKloskies or General Finishes polyurethanes. Both are excellent and infinitely easier to work with than Minwax.
I suffer from CDO ... Its like OCD, but in alphabetical order, LIKE IT SHOULD BE!!!