Unfortunately, going by all accounts we've heard over the years here, PayPal's front-line customer service agents don't seem trained or equipped for actual tech support (that's what MTS is for), and their longstanding track record of buck-passing and uninformed wild guesswork suggest their staffing metrics may prioritize quick answers over correct or responsible ones.
As for MTS, the cryptic info in their latest response was too vague to be at all helpful, if it's even relevant to the issue at all, so I've asked them to clarify. BTW, our case number is #09397939 for that MTS ticket, not that PayPal customer service is likely to be able to do anything useful with it.
Nothing at our end changed to account for this emergent issue, and we're still doing everything correctly in compliance with their current technical documentation. Just as you say, their system clearly has applicable tax/shipping amounts -- they're getting reported back to us in IPNs after payment -- and their checkout site just isn't adding those amounts to the buyer's final payment total.
That payment total gets calculated at PayPal's end without any influence from us once the buyer arrives there -- especially now that we're not even asking PayPal's system to callback to ours to recalculate tax/shipping, and even when we did, they'd still have the precalculated fallback amounts from our cart to apply in case the callback ever failed for any reason.
That was all working fine until early last week, so if nothing changed at our end, and nothing changed in their technical requirements to integrate with their end, which suddenly started sporadically failing to properly add up all the amounts we are correctly transmitting to them, the problem must be due to something that changed at their end, which they have to fix.