From what I can tell, there's a bug with the new lowered values for rapport thresholds.

Here are the new values with the old values in parentheses:

Default: 750
Friendly: 1000 (1500)
Close: 2000 (2750)
Allied: 3000 (4000)
Companion: 4000 (5000)

It seems that if you had between 4000 and 5000 rapport with the companion when the patch dropped (so Allied under the old values, but not yet Companion), the menu displays you as having Companion-level rapport with the companion and their dialogue is correct, but you don't get credit for the achievement. It's possible that this is because the achievement progress is triggered specifically through gaining rapport that pushes rapport from Allied to Companion, but if the companion's rapport was already at 4000, this technically never happened, since the rapport threshold changed without any actual change in rapport.

Based on another thread, I believe it can be fixed by doing actions that decrease the companion's rapport until it falls below 4000; then you can do things that raise the companion's rapport back to 4000.

Isobel most dislikes murder, but unfortunately, it only lowers her rapport by 10 and there appears to be a cooldown during which it only decreases her rapport by 1, so it will take a lot of killing to annoy her enough to drop her below 4000 rapport, since you seem to be maxed at 5500.

You can check the companion's rapport value with /script d(GetActiveCompanionRapport()) in the chat window.

I've seen this reported for Mirri and Bastian, and now Isobel, so presumably if affects Ember, as well.

Decided I'm just going to suffer with her longer on a new toon and raise her rapport up again...seems easier than lowering and rebuilding (and I already know that when I'm done, they'll fix the big haha)