I'm not sure how you didn't get the "secret keeper" achievement if you found the "ultimate secret." Simply entering the room triggers this text (the code changes the text color):
[c/FF9900:Ultimate Secret Area Discovered]
[c/04ba13:Khaios: Congratulations on getting here! You've earned this prize! I hope it helps you with finishing up the map.]
[c/FF9900:Achievement Get: Secret Keeper]
And it activates the achievement counter. So if you saw the text "Ultimate Secret" then you definitely triggered the secret keeper achievement.
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As for the "reward chest" you were asking about, either you miscounted, or plantera bugged once and didn't spawn (which has been known to happen on occasion). There are definitely 10 spawners.
Worry not! It was just a troll event, haha. The only thing at the end of the chamber would be a Red Potion. So no actual rewards or achievements were missed. I was planning on throwing a real reward and achievement in that room, but when I found out there was a chance for plantera to not actually show up, I had to adjust my plans.
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It would be helpful for me to take a look at your world save, if you say you got more achievements than it gave you. I won't be able to confirm that or figure out the problem unless I take a closer look.
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And as for secrets, looks like you missed:
One somewhere in the final parts of the portal chambers
One somewhere in the forge
One secret within a secret area (I'm evil, I know)