I would think that anyone hiring a Ph.D. in Computer Science would be looking for a different kind of output than the knowledge of actually doing software development and the associated project management/time management work. I would imagine that such people, if placed optimally, would be doing largely self-directed work with an expectation of solving a very complicated problem, with work output that looked more like a thesis than a program.
I further surmise that very few companies need these kinds of people. If your needs are people that can be managed to do basic programming tasks (my job as well), then that's what you hire. That's something like 99% of all programming work.
It's like hiring someone that understands the building of nuclear power plants, and being surprised that they don't understand basic home building codes.
The saddest part of it, for me, though, is that someone with a Ph.D. in Computer Science that is searching for a job in the non-research sector is probably having a really bad time. Research is happening, but I don't think it will jump in a very large way until there are a lot more dollars being pumped into research using public money.