This whole discussion reminds me of the cranky old "clubfitter" guys who want you to bring your brand-new Titleist or Callaway irons in to "check the frequencies" on their meter. They'll show you how they may be marked "S" but some of them have higher frequencies than X-flex hard-stepped and others are almost as low as Senior. That's why you ought to have bought some frequency matched, spined, PURE'd, custom blueprinted Hireko irons from them instead.
I'm no crusty old clubfitter, but I've seen what you describe with my own two eyes. A few years back a friend had a TM driver with the stock Stiff flex shaft in it. Couldn't hit it to save his life and after several rounds with it not performing he almost tossed it. We had a demo day and a local club-builder with a mobile shop was there. My friend asked him about his experience with the club and the builder said bring it to me.
He put it on the frequency machine and it came out at a soft senior flex. The builder offered to swap it out with one he knew was a Stiff flex and my friend accepted. He took it to the range and starting hitting it well. It was a whole new driver.