Hector Martin

You're using 2 channels on the interface (files are stereo). It has a hardware level meter. The level meter always shows activity (in both L/R channels), even when playing 'B', regardless of whether it worked that time or not. When playing both files, mixing is done in software.

It's not a stereo cancellation issue: you can hear both channels and it doesn't sound like 'A' is suffering from cancellation. It's not a software channel routing issue: you've verified that both files mix into the same two main outputs, every time.

What is this sorcery? How can one file show up on the level meter consistently but only output sound half of the time, while the other file always works? Hint: 'B' was recorded earlier on the same interface. I already figured it out, but any guesses?

the same interface 'A' was recorded on, or the same interface they're being played on?

The same interface they're being played on.

is there an extremely evil resampler or DAC (or its conversion from PCM to delta-sigma) involved? or is there some sort of extremely evil in-band signaling?

my first thought was "maybe if on input something upsampled by inserting 0 every other sample, and on output something's downsampling by dropping every other sample, so it works half the time and is completely silent the other half"

which should be too absurd to even contemplate but I dunno, I've seen some extremely bad audio hardware and software