Well, I explicitly said there's obviously something going on, so we're in agreement there. There's no motivation for Jerry to hire trainers and then disregard what they prescribe. Why would he do that? There's a simpler explanation somewhere, we just don't have the visibility into the organization to know what it is, yet.
Some of these injuries: Crawford's achilles tendon, for example. Or Spencer's knee condition...these things are just bad luck. Ratliff's issues were very likely emotional and not a legitimate physical injury taking too long to heal. And, obviously, every NFL team deals with a fair share of injuries every season. If we're a few standard deviations to the right of the injury curve the last two seasons (and I really don't have a grip on the scale of how our problems might compare to the rest of the league), it's probably related to the soft-tissue injuries we seem to get so many of.
I don't know what the explanation might be, but I also haven't heard too many plausible theories. Who determines the team's stretching regimen, anyway? Trainers? Strength/conditioning coaches? The head coach? I do recall commenting when I went to camp how haphazard and half-hearted the warm up stretching period was. Players who wanted to stretch would apply themselves aggressively, but there were other players just going through the motions. It looked like my high school warm ups so much that I thought it was weird that a pro squad wouldn't take it more seriously.
Obviously, this is just something I pulled out of my backside, and I don't think it's something as easy as 'stretching better' to fix the problem, but I do think the problem has a physical explanation somewhere, and it's going to be something more practical than 'Jerry Jones says we don't have to do what we don't want to do.'