Dear eojk:
I'm very sorry to hear about your problems with your Yojimbo. I was not aware of any redesign of the detent recess, but when I pulled out some of my older vintage Yojimbos and compared them to some recent ones I purchased, I noticed the difference as well. The only thing I can speculate is that, since the liner doesn't index deeply into the recesses in the old ones, they changed the depth of the cut to eliminate the unused space and simplify the machining process.
Again, that's just speculation. The bottom line is if you're not pleased with your knife, you should return it for repair. I've always had great experiences with Spyderco's repair department (long before I was associated with them as a designer), so I'm sure they'll do you right.
A couple of other points:
1) the improved clip design is actually the original design that I provided. The hole is the same size, but the body of the clip is wider to put more steel on each side of the hole. I actually provided a handmade clip with my concept model of the knife and Spyderco chose to narrow it. Once they started getting returns for bent clips, they redesigned it to match the original.
2) The safest way to carry a tip-up folder is to seat it all the way back in the pocket so the back of the blade rests against the inside of the pocket in line with the seam on the side of your pants. This not only keeps the knife in a consistent position and orientation for a reliable draw, it holds the blade closed even when the detent doesn't. I learned this lesson the hard way with several tip-up liner locks.
I hope this helps. Thank you all for your confidence in the Yojimbo and your kind words about my design.
Stay safe,
Mike