If you're getting that message, /recountnuts will not work, iirc. That isn't determined by the nut count. What the command does is recheck the count against the found walnuts and fixes the count. The parrots messages don't check the count, just the found nuts.
What this means is that you're seeing the parrot say anything, you absolutely are missing a golden walnut.
The walnuts that come from journal scraps:
1 - the one dropped from a tree by the volcano when shot by a slingshot
2 - the dig spot just north of Birdie's hut, dug up with a quality bobber
3 - the dig spot in the SE corner of the island farm, dug up with a pearl
4 - the dig spot SW of the volcano entrance, dug up with an ostrich egg
You are missing one of these. You said you double checked all 3, but you can see there are 4. If the count says you're missing 2, /recount nuts might change it to 1, but you absolutely are missing at least 1. I don't know which because you didn't say which scrap you missed.