I just reported this to Thom, and sent him my logs, but I wanted to make sure other sellers knew about this in case it affects them.
Sometimes after 7/29, the "make this item eligible for shipping discount based on my ebay preferences" apprears to have stopped working for me. Thom checked my logs and the "toggle" is, in fact, being sent to Ebay. But the resulting listing does not have the option checked.
I've been able to do a batch-update via Ebay and turn the option back "on". I only discovered the problem after having to refund several customers who were over-charged shipping. The preferences themselves are set correctly at ebay - it's just the "on/off" toggle on the individual auctions that seems to be the problem.
Everything listed prior to 7/29 seems to have worked fine, but currently I can't get any store or fixed price auctions to list with the ebay shipping discounts turned on.