Services Entity REST Application - Update (via put) Field Collection Data
It appears that something to do with revisions is causing the problem as if I provide specific (required?) data in my PUT request it works. Working PUT request JSON:

{
    "field_primary_aircraft": {
        "und": [
            {
                "value": "1"
            }
        ]
    },
    "field_name": "field_aircraft",
    "item_id": "5929",
    "revision_id": "5929",
    "default_revision": true,
    "field_aircraft_registration": {
        "und": [
            {
                "value": "testing12355"
            }
        ]
    }
}


That JSON plus a working CSRF token allowed me to save data back to a field collection that  is part of a users Profile2 profile.

The revision_id and default_revision were the trickiest parts to track down and supply, I don't have revisions enabled as far as I can tell also, so why this problem started suddenly I have no idea...at least it is solved and hopefully this info helps someone else.