All three of the ones that changed to dream ball had an 86h of 19, which overwrote the 83h to 19.
If you opened them up in a hex editor (HxD) and changed the 0x86 location to 00, you should be fine. Save the new file (new checksum doesnt matter) and then shift the new file.
I checked data from other PKMs I have (Heal Ball, Quick Ball) and they didn't have a 86h=19. I don't know about the Ninetails either, assuming it was bred.
Just wondering, did you ever put them in ball capsules? If you did, were they still in capsules when you grabbed the PKMs?