UPDATE 10/11/14 2:55pm CST: All customers who were affected by PayPal's bug have been notified with a list of orders to review, plus some tips for how to resolve the issue. Some customers report that they've been able to get PayPal to pay for the shipping fees that weren't collected -- it's worth a try.
As we've done all we can on this, and the bug has been fixed at PayPal's side, we're going to consider this issue closed. As always you can open a support ticket if you need help on this matter.
UPDATE 10/10/14 4:00pm CST: Unfortunately there is still some fallout from PayPal's error yesterday.
An IndieMade site doesn't mark a PayPal order as payment received until it gets notice from PayPal that the entire balance has been received. Because PayPal was simply ignoring shipping charges for about a day, those orders are now stuck in the pending state: the IndieMade site is expecting the funds it asked for shipping, but that money simply isn't coming because PayPal didn't ask the customer for it.
Unfortunately PayPal's policy on this is just to ask IndieMade site owners to send their customers invoices for the additional shipping.
We're working on a tool that can automatically identify orders that require attention from IndieMade site owners, so our customers can decide how best to handle this situation. We'll update this ticket with further details when we have them.
UPDATE 10/10/14 1:18pm CST: PayPal has fixed the problem with shipping, so we've reversed the emergency patch we put in place yesterday. Shipping and handling fees are now working as they did before.
Earlier today we received some reports that shipping wasn't being properly applied at PayPal. We contacted PayPal support and they acknowledged that it's a bug on their side:
Unfortunately, the problem you are experiencing is being caused by some technical issues with the PayPal system. Our engineers are currently working diligently on a solution to this problem.
Until they have this fixed, we've put an emergency patch in place that treats shipping as a separate product (rather than a different category of payment). So cart totals will be correct. As soon as PayPal fixes the problem we'll reverse the emergency patch.
I'll update this status message as we get new information.