The shortcut for Subsuperscript doesn't work?

It appears that when you use Control-% to create something that looks like $x_a^b$, the underlying box representation will be a SubsuperscriptBox. However, the interpretation of a SubsuperscriptBox["x", "a", "b"] box is the expression Subscript[x, a]^b. The expression Subsuperscript[x, a, b]is formatted as TemplateBox[{"x","a","b"}, "Subsuperscript"]] in StandardForm.

As you noticed, as of version 9, the documentation doesn't match the actual behaviour.

Can you contact WRI about this so they can sort it out (either on the documentation side or the software side)?

If you want to have SubsuperscriptBox parse as Subsuperscript instead of Power[Subscript[..], ..], you could do the following:

Unprotect[SubsuperscriptBox];
SubsuperscriptBox /: MakeExpression[SubsuperscriptBox[x_,y_,z_], f:StandardForm] :=
Thread[
    Subsuperscript[
        MakeExpression[x, f],
        MakeExpression[y, f],
        MakeExpression[z, f]
    ],
    HoldComplete
]
Protect[SubsuperscriptBox];