I've encountered a glitch where I've successfully completed the entire game but I still have five achievements locked. The achievements in question include -
Festival Master - (Completed both tournaments with gold status at least 2 times each.)
4 Secret achievements -(I looked them up after completing the game)
A Stormdog's Bond - (story based so impossible to miss)
The Red-Haired Enigma - (story based so impossible to miss)
Ancient Sentient Support - (story based so impossible to miss)
Custodian of the Scrollroads - (Have completed this and should be evident with the other achievements like Great Wave Alumni & Owl Tide Bestiary which I unlocked)
Now for the details on where I suspect things went wrong. Since my achievement progress stopped right before the story based pick up of Taika I believe the issue was caused by my save of my game progress from the initial slot 1 into slot 2 mid way through the game.
In more detail, I was at the last frog statue before facing the Gobking in the goblin camp. I had loaded the game up from continue at the start menu and then went and battled the Gobking. After defeating him I immediately went back to the same frog statue and choose to save in game slot 2 as I was worried that since I didn't try to steal from him that I might have missed some sweet loot. After saving I continued the story and progressed into the burning sands to the point that I had freed Taika and defeated Sharaan. After this I went to the island and farmed for bit then saved using the quick save slot 2 option at the island frog statue.
The next time I loaded up the game from the continue option, I noticed that when looking at the options in the frog statue the save quick option had changed slot # to 1. Which instantly made me wonder if the game had some how overwritten my progress on the slot one. When I went to look in more detail I found that my old slot 1 had been pushed down to slot 2 leaving it with the same progress percentage I had been at etc.
It was until after I had made it all the way through scrollroads that I realized the achievements hadn't been going off for quite some time. I then looked at the Xbox one achievements page and noted that the progress to complete amounts was off on several achievements. Most notably the Heroic Hoarder was at 0% and I had acquired 2 of them already.
At this point I went to a frog statue and saved over my old slot 1 (now in slot 2) progress to see if bringing it up to speed with my current status would some how unlock everything. It did not but I still believe this fixed things in the long run as it did update my progress in some areas like Heroic Hoarder, Lango Plantmaster and Owl Tide Bestiary. From that point on I was able to gain achievements that were story based again but never gained those state above.
Sorry for such a long post but I wanted to be as descriptive as possible in hopes it would help to narrow down the issue. If anyone wants to confirm based on my account, I use the gamertag of xII Kingz IIx for Xbox. I've also attached a cropped screenshot of my achievements from Xbox.com. I won't go back and get these achievements for sometime in hopes it helps snowcastle.