Update: I fixed some credientials for a paid shipping plugin I'm using. Not sure how that ties in, but after the fix, I noticed Paypal did have a discount line. However, the subtotal is still wrong. Like this:
Product 1 $10
Product 2 $10
Subtotal $15 (should be $20)
Discount $5
Total $15
The subtotal is incorrect. What in the world is up with that?