I have a few things to say about all this.
Trust that if you can see the stuck diaphragm, you should return the headphone. It is broken, and not sounding as intended. EQ is an extremely powerful tool in my opinion, and our brains are super malleable when it comes to "accepting" a sound signature that's flawed, especially if we've deceived ourselves that what we are hearing is "correct". I literally just went through this experience myself with the HE6se, and was so in-need of an auditory "compass" that I spent an additional 600 bucks on a second set of these things just so I could be damned sure my set was 100% functional. It wasn't. But I was second guessing my own ability to tell, and with the proper EQ I too was getting a sound signature that was pretty darned good. It was spacious, and the imaging was really, really good. I also have a Clear, and I know exactly what you're saying about the staging comparison.
But, when I got my replacements back I was absolutely blown away by the difference in sound. With stuck drivers it is possible to get a workable sound with (mandatory) EQ, but with functional drivers this headphone is totally EQ optional, and sounds fantastic. The bass is rich and deep and well extended right out of the box. This was the most obvious difference to me. You won't second guess yourself once you've heard a working HE6se. You'll know it when you hear it.
Package 'em up and send 'em back! Trust me on this. You won't regret it.