I’ve run into the same problem as well.
However, I’ve managed to find what the issue is. If I set the price of something to for example: 18.325 (so the price after tax would be 21.99), then it charges tax twice on PayPal. If I set it to 18.3249, then it works perfectly, and only charges tax once. I think WooCommerce doesn’t round prices the same way as PayPal does, so that’s might cause the issue.