ok.
so everything else is nulling. this isn't an old problem that i didn't notice. i can have faith in my ears, which seem to be quite sensitive. i don't have to go back and fine comb anything.
i'm running the null tests a little further past where i did before, and i'm noticing that a pattern is developing: it's the first two tracks. always. the rest always nulls.
it's also becoming apparent that the break didn't really happen until about five tracks in. in hindsight, i think i dropped some effects work on the third and fourth, but i'll have to see if i can recreate it; i vaguely recall playing with a quadrafuzz. they're not fitting the pattern - they just seem to be missing distortion. i remember re-rendering the second because it didn't sound right [that would have been the first time i noticed it was broken], so the earliest version i have of this isn't clean. from the fifth on, i get the pattern with the first two tracks.
...which means it couldn't be the codec install, because that was a lot earlier.
i still can't explain why the first tracks are always broken, but given that it's consistent it's starting to seem more like a broken cubase.
but i'm now starting to wonder if the clock issues might be related to the constant stretching i was doing. i sent these files in in such a way that they're subtly out of sync. i then had to carefully stretch them back in sync through trial and error. could i have broken the clock in the machine?
a firmware reset in the device is a useful troubleshooting step, i just don't know if this is possible.
i'm going to finish running through nulling the sequence, and then see if i can at least get consistency over the set of new files.