Thanks Anish, sent that along. Just to be clear- this configuration has worked and still works with all other Alexa footage, and I haven't seen this problem with any other footage from any camera...
My workaround was (ugh) to read the "media start" on the transcoded dailies and use "change timecode" to specify the media start on the camera originals. Many hundred of times. While doing that, we noticed some oddities in the camera original footage. Occasionally the camera recorded exactly 9-second takes of green frames...it's unclear if the camera rolled or if it was writing these clips to the cards without rolling. On those clips, the time resets to 00:00:00:00.
There's definitely something wrong with the clips from the camera, but in the end we seem to be able to get the picture in by manually putting in the timecode and extracting reel numbers from file path...
KC
Prehistoric Digital