I am not aware that USPS charges sales tax on shipping, as the shipping charge is a postage (similar to buying a stamp, you don't pay sales tax on stamps).
What I meant about paying to CA was that if the shipper is charging sales tax on an order, and not keeping detailed records of separate charges, then they must remit to CA whatever sales tax they collect. They should not be charging customers sales tax on shipping and then pocketing this extra money.
And yes, you are correct, that if the company is charging shipping costs that are more than the actual cost of delivery to the client, the overage is taxable as "handling" charges. A common practice for businesses is to either combine shipping and handling, or say "free shipping" but charge a larger handling fee. It seems as though this merchant is doing something along these lines, and probably considering that lumping your purchases together is handling.
If it makes a large difference, I would ask the company for a refund on the tax on the actual shipping charges, which is what the company paid for deliver fees. You can cite the brochure and the information on shipping charges and "actual cost of delivery not taxable" as state guidelines. If they refuse, you could tactfully tell them that you are going to call the CA board of equalization with this information, just to make sure that their practices are legal.
I wish you the best of luck, and I understand your frustration. It seems as the business owner benefits by keeping "undetailed" records and calling everything handling.