WOW, holy crap.
It looks like it probably was a word wrap thing. I'm working on something unrelated to CW or transcription right now, and I've noticed some very strange things happening as I try to use text that I wrote in notepad. Line breaks seemingly entered somehow (?!) even though I never would have broken the line in any of those places. This kind of blow my mind. I can't be completely sure that this happened with CW, as everything looked solid in the "preview" area in the HIT itself, but clearly something strange is going on here.
This is a new laptop, but I've never seen something like this happen with notepad before. I thought notepad was supposed to be the kind of spare formatting?!
[runs off to tinker]
So there's a bug in the current notepad that inserts all kinds of line breaks if you save with word wrap on. And so instead of having a document with minimal formatting, it made it as if I had inserted all those breaks myself!
Saving with word wrap turned off (but not manual line breaks inserted anywhere) results in perfectly clean text.
Seriously, just kill me. Obviously this is what I get for upgrading my ancient machine. Maybe I should go back to being several OS releases behind the rest of the world.
[waves the white flag]
However, thank you for the great responses everyone. I got some pretty great tips out of all that, in any event.
I tried incredibly hard to make sure that was a quality transcript, too. All that work, only to be foiled by a computer bug.