I prefer to use UPS and only use USPS when UPS would cost too much. I haven't had breakage though with either, but feel better with UPS. Like you, I wrap each one in bubble wrap, going around twice in the front. I then place these stacked on their sides on top of peanuts on the bottom, bubble wrap above. On top of the cookies (which have more bubble wrap in the front of the stack and at the back) I do a layer of bubble and peanuts. Same for the sides. Were you placing them on their sides? Maybe that is the trick.
I used to put one box inside of another with a layer of peanuts surrounding, but have found that wasn't needed. I print out a label that says "FRAGILE - TOP LOAD ONLY" for the UPS boxes. As for whether or not they read it, I do not know, but I feel I have a better chance with UPS reading it than USPS (I give the UPS guys cookies when I bring a box it
). The first time I droppped a box off at USPS, I told them they were fragile and watched them put the box on a chute and saw it drop down into a bin. Thunk.
For cookies that have a fragile shape (wine bottle, electric guitars), I place a piece of cakeboard in the cello bag to protect the fragile area. If you do this, just put a piece of parchment paper in between the cookie and the cakeboard to prevent butter staining.
So sorry you have had breakage!
I don't ship a lot, but of the two, I prefer UPS.