The card says "skip your next turn" and not "skip your next turn on the turn structure table." In other words,
Now, let's say my first turn is as follows: Land, mox, Time Vault.
I skip my turn and put vault's ability on the stack. The turn chart now looks like this:
1*00101010...
Vault's ability resolves and it gets untapped and gains a time counter. I then tap it and remove the time counter to take another turn after this one. The turn structure now looks like this:
1*1001010...
That bold number is where your problem is. You don't ever take that turn, because Time Vault told you to skip your next turn. That bold number is your next turn.
EDIT-beat to it.
This should also be in the rules forum, since it is a rules question.