Nothing new to report. Every time I followup on our MTS ticket to ask for a status update, they just say they're aware of the issue and have escalated it to their engineers who are working on a solution.
Received the following reply from PayPal Global Technical Support regarding my inquiry about this problem:
"Our Engineers are currently working on temporary measures to address the issue. The problem is twofold between eJunkie, and PayPal related to the way our Integration has changed over time and eJunkie not adapting to those changes as intended. I believe the plan is to roll back some of those changes, but I am still wanting on a confirmation on that situation."
As I read it, this blames e-Junkie.
My response so far has been to no longer use PayPal with the e-Junkie cart.
Interesting, this is the first we're hearing anything about "eJunkie not adapting to those changes as intended", assuming that's not just a buck-passing excuse. They certainly never informed us we needed to change or update anything, and our PayPal integration is still fully compliant with their current documentation for it.
@mbw - We'll followup on our own MTS ticket to inquire further about that with PayPal; what's your MTS case #, so we can reference that in our followup?
The case number is 10200744. I opened it on February 7, 2022
Here's the full email:
Dear M B Walker,
Our Engineers are currently working on temporary measures to address the issue. The problem is twofold between eJunkie, and PayPal related to the way our Integration has changed over time and eJunkie not adapting to those changes as intended. I believe the plan is to roll back some of those changes, but I am still wanting on a confirmation on that situation.
I will update you as soon as I know more. I apologize for any inconvenience.
Thank you,
Brian
Global Technical Support
PayPal, Inc.
Here's how PayPal MTS responded to my followup seeking clarification re: "adapting to changes as intended":
Our engineers have figured out the root cause of this issue that is caused by our system. They are currently working on a resolution to this issue. And I was not informed to have you make any changes in your integration. So you don't need to change anything at this time. If I have any further updates on the matter will let you know.
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
9 days later
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.