i will try and track down exactly what causes it, but I ran a script last night to have photoshop open all my photos, and save them at "level 10" compression. This shrank many of the photos, but plenty of them are still above 2mb, plenty of them are above 3000x2000px . The metadata refresh worked on all of them, as far as I can tell.
I will try and create the smallest image that will fail, and then save it through photoshop so there is a version that works.
I read that in the future imagemagic may be an option, is that still in the works?