I'm not familiar with the actual ejection systems. But what you want a FDR to capture is attitude/altitude/speed etc and systems information. So when you have some kind of catastrophic incident you can identify the failures that led up to it. Were I designing that system it would be completely automated as no flight crew is going to even be considering FDR, nor should they. Also possible that it's structurally designed to separate on impact. For example, it stays in the plane until the moment of the crash, but the force of the crash compromises the installation of the box to separate it from the aircraft. Kind of like the intentional version of high speed car crashes with unbuckled passengers that get thrown clear during the crash sequence.