@Neuro's suggestion I pulled all the EXIF data with exiftool (handy utility that). There are many difference between shots, obviously, but two discrepancies that I cannot explain (just looking at two photos, let's assume that pattern holds)
In the overexposed shot I have:
AE Setting: AE Lock
Raw Measured RGGB: 0 0 0 0
For the properly-exposed shot I have
Raw Measured RGGB: 142716 283278 285415 128586
and I have no entry for AE setting.
I have no idea why the Raw Measured RGGB data is all null for the overexposed shot but the AE lock does tell me what the problem with that exposure is. However (and I just tested this and it work properly) one must hold down the AE lock button between shto carry the exposure through multiple shots. While I might have accidentally pressed this button I'm certain I did not hold it down for those three shots. I'm guessing that microswitch is sticky.
At least I know what to do to get out of that problem now. Thanks for the suggestions folks.