With the Necrom update, the amount of rapport needed for each level of positive rapport was lowered. I've been using /script d(GetActiveCompanionRapport()) to check when quests become available. Here are the current numbers with the old required values in parentheses:

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

I wonder if, because Mirri and Bastian are older companions, the achievement is checking for a value of rapport rather than the relationship level (that is, for 5000 rapport rather than "Companion" rapport level).

All my older companions have 5500 rapport with my main character, the old maximum amount. I don't know whether rapport is now capped at a lower number and whether this impacts the older companions' achievements and dialogue.

Do Mirri and Bastian give the correct dialogue when spoken to and asked about your relationship? I've linked their UESP pages which has the dialogue for Companion-level rapport.

Also, since required rapport for each relationship level was lowered, can I ask a bit about your rapport levels with Mirri and Bastian prior to the patch? Essentially, I'm wondering if you had their rapport at less than 5000 but above the new threshold for Companion-level rapport, and the UI properly shows them at Companion-level rapport but it doesn't count for achievement because you didn't hit the threshold "naturally" (that is, gained rapport that pushed them over the threshold). In that case, maybe gaining rapport on each would properly update the achievement?

Well I hope they can get it working for you!