An easy counter-example via the Pauli matrices not commuting and being their own inverse. Not sure if you'll consider it cheating.
Note that:
##[X, Z] = 2iY##
##[X^2, Z^2] = [I, I] = 0##
##I## has many square roots, ##X## and ##Z## among them. We can pick different ones for ##A## and ##B## when setting ##A=B=I##. So ##[A, B] = [I, I] = 0## but ##[A^{\frac{1}{2}}, B^{\frac{1}{2}}] = [X, Z] = 2iY##.
I guess technically ##[A^{\frac{1}{2}}, B^{\frac{1}{2}}]## is not really well defined here. It's a multi-valued function, but some of those values aren't 0.
It might still be the case if we restrict ourselves to the principle powers of a matrix. Require that ##A^x## be interpreted as raising its eigenvalues to ##x##. Further require that ##(e^{i y})^x## only allows the ##e^{i x y} = \cos(x y) + i \sin(x y)## solution. Not so sure in that case.