Well, obviously they won't help.
But I'm much more optimistic. I think you'll be fine. With such a rigorous coarse load I think you'll be forgiven. Of course none of us can really say for sure. I highly doubt that those few discrepancies would negate the lovely parts of your application and four years worth of other achievements.
I'm in a similar boat. I got a B+ this year in AP Calc BC. It's my second non A for high school. (Had an A- freshman year). My school doesn't weight.