Kirk didn't appear to remember his exact moment of beamdown in "Mark of Gideon" - or, in other words, he and the audience witnessed a beamdown into an empty transporter room, but later events in the episode revealed that Kirk had in fact been medically treated after his actual beam-down and before the scene we saw. But that was probably because the Gideonites used anesthetic and perhaps also amnesia-inducing means on the hero. It was not the transporter's fault.
Beyond that, I don't recall the device knocking anybody unconscious, not for real. Beaming between universes didn't hurt or discomfort our heroes in TOS or DS9, either. But beaming from one century to another is a unique event, and who knows what else it did to the poor bodies of our DS9 heroes!
Timo Saloniemi
