I didn't get it fixed but I did figure out a workaround.
After rendering the flash particle on its own I then rendered out 2 sequences for the smoke. One had the emitter set up as normal. I then changed the color of the emitter to a gradient of white to black. I use the second sequence as the alpha for the first one. There's still some popping at the end, but it's manageable in post now.
I'm looking into this, and I can't figure it out. It seems like something in that particle type got "goofed up" somehow, but I can't figure out what.
Nothing I change seems to fix the problem, but I can create a new particle type (in the emitter props dialog, select the emitter in the hierarchy, then click the "new particle type" button), and the new particle type behaves correctly. I've never seen anything like this. How did you create this emitter? Was it built from another emitter?