I’m having this same problem on Spotting Giant Sea Bass. When I enter an ID in the field under Add to existing individual ID (e.g., “GSB178”), there’s no way to “set” or confirm the entry, so it just disappears when I hit Close Edit. I tried hitting the Enter key, as well as clicking “set” next to both the Matched by and Set Alternatve ID fields, but that didn’t do it. I expect to see a checkmark next to the dialog box once the ID (GSB178) is entered. I tried this on a few other encounters, as well as in Chrome Incognito mode, but no dice.
I didn’t get the same message you did on Manta Matcher about repeated annotations.