I have followed your advice gone back to defaults and reloaded the snapshot. The default setting includes all the fields. After I reload the snapshot the fields A) Special Instructions & B) Transmission Reference disappear entirely from the Customize IPTC Stationery window although they are on the IPTC Stationery Pad and the IPTC Info window. On the Info Window they are in the right place but on the Pad they are not and I can't find them on the Customization window to move them.
The Rights Usage Terms are on all three windows all the time so I might have incorrectly included them as part of the bug.
When I first experienced the problem I lost about 4 fields as I moved them. They were missing from the Customization but were on the Pad and Info windows but to the bottom of column 1 on the Pad but in the right place on the Info window. I then reloaded the defaults and started again this time taking a snapshot which you have but only losing 2 fields as I didn't try to move any more.
My purpose of moving the fields was to keep all the altering fields together at the top left of the Pad.
Are you saying that the two fields A & B are now on your customization window with that snapshot?
In an earlier post you said that you were likely to remove the Classic IPTC window entirely. I, for one, would not like that as I can now tick the Classic box and I am back with the Classic IPTC, without loading snapshots or unticking boxes, which the agency I work with expects me to use.
I hope this helps.