The delayed downloads issue was due to an IPN delay at PayPal's end, which we announced at the time in our System Status forum here:
Back to the main topic at hand in this thread, at present we have to pass any calculated shipping amounts to PayPal as a 'handling' value, as 'shipping' values can only be applied during checkout on PayPal's site, not in the cart before checkout.
About a year ago, PayPal introduced a new shipping recalculation feature, where PayPal Standard checkouts could call back to our system to verify accurate shipping amounts based on the actual shipping address provided at checkout, so we started supported that. However, this new feature turned out to behave rather erratically in practice, so last winter we had to revert back to the old method of passing a pre-calculated shipping amount as 'handling' until things could get sorted out better.
Bear in mind, all the above only applies to PayPal Website Payments Standard, not Website Payments Pro, which uses an entirely different method to handle the order data for checkout. If you noticed a change when you upgraded to Pro, or downgraded from Pro back to Standard, that would probably explain the matter.