Received this reply from PayPal support:
Hi Dale,
Developers have resolved this issue. Please confirm resolution by replying to this ticket. Thank you for your business and I hope you have a great day!
Sincerely,
Jeremy
Global Technical Support
PayPal, Inc.
I followed up on our own MTS ticket to verify that this bug is indeed fixed. They replied Friday evening to clarify:
We have made the fix, but it is going out in the next release cycle which should be within the next week. We will restart the experiment and monitor after the release has finished to make sure things are working properly. Will let you know once it is done.
PayPal MTS has now confirmed the fix was rolled out to live production last night. Let us know if you encounter any problems going forward. Thanks again to everyone for your patience and cooperation in riding this out.
Ahh!!! This is all good news!!!! I'm ready to get my shop up and running again!!!! But just real quick, can someone confirm that's made a sale that everything is ok?!?!?!? Thank you in advance!!!! -Eric
I'm using again!!! And it looks like everything is ok!!!! Made a couple of sales with no problem!!!! Hope this helps!!! -Eric
Issue has returned. 350 transactions (ish) today and probably 10 have had no shipping charge added. Same thing as before.
Oh dear. 
We'll open another ticket with MTS about that.
It would help if you could email us an affected Transaction ID and, if possible, the IPN Message for that transaction, which you can copy from your PayPal IPN History -- for instructions to access and copy that IPN Message, see Part C, Step 2 here:
Is this still happening? I thought it was resolved? I was about to change back to PayPal but now I'm not sure.
It was resolved, until @mdgbv reported a regression of the issue for them last week, though they're the only one reporting that so far.
As for the new ticket we opened with PayPal MTS about it (case # 10666290), they confirmed Sunday night they'd escalated it to their engineers for correction, still awaiting any further updates from them about it.
Everything was working as normal for me until this afternoon when I received an e-junkie fraud alert showing that tax and shipping is not being added to the subtotal in Paypal (again!). This is the same issue that's occurred twice before. Is this an issue just with Paypal Standard Payments or is it with all Paypal payment options?
@halfahundredacrewood - Please forward a copy of that Suspected Fraud email to support@e-junkie.com, so we can add that case to the ticket we opened with MTS about it. Thanks!
This issue can only affect orders where buyers go through the PayPal checkout site to pay, as that's where PayPal is failing to add the calculated tax/shipping amount(s) to the buyer's final payment total -- i.e., this only affects some buyers using the Pay Using PayPal checkout button for sellers using PayPal Payments Standard, PayPal Payments Advanced, or PayPal Payments Pro.
Buyers who use the Pay Using a Card checkout button (whether handled by a PayPal or any other payment gateway) would be unaffected, as there (unlike PayPal checkout) we have full control over calculating the final payment total and won't let buyers enter a shipping address with a different country/postal code than they'd specified in the cart.
