You're not crazy, and you're not alone. I finally got around to performing a few mods a few days ago, and while I was too conservative, they changed the sound enough to make my T50RP's sound decent. I listen relatively quietly (sometimes very quietly), but I noticed a feeling of pressure and dull discomfort pretty much the first time I listened to them extensively, just like you. I feel it right now in my left ear, which is what brought me back to the forums this morning...and lo and behold, someone else is posting about it. It's tolerable for me, but I am a little vaguely concerned about whether something might be causing damage.
I feels good to know that I am not crazy.
I really think it's weird. Right now the headphone is playing a few feet on my left (quite loudly, I am burning it in), and I actually felt some strain on my left ear!
I think it's getting better for me, I don't know if I am developing resistant to it, not a good thing if there is indeed something wrong with this headphone.
Btw, what amp are you using? I wonder if my amp is having some kind of oscillation and that produces ultrasonic noise.