You're dealing with different charge densities in each equation. When you write $$\oint \vec{E} \cdot d\vec{A} = \frac{1}{\epsilon_0} \iiint_\Omega \rho \ dV$$ the ##\rho## is the total charge, i.e. the free charge plus the bound charge, whereas the proper equation using the ##D## field is $$\oint \vec{D} \cdot d\vec{A} = \iiint_\Omega \rho_f \ dV$$ using only the free charge.
More explicitly, starting from the equation for the ##D## field, let ##\vec{D} = \epsilon_0 \vec{E} + \vec{P}##, so substituting this in:
$$\oint \vec{D} \cdot d\vec{A} = \iiint \rho_f \ dV \Rightarrow \oint \left(\epsilon_0\vec{E} + \vec{P}\right) \cdot d\vec{A} = \iiint_\Omega \rho_f \ dV$$ Then $$\oint \epsilon_0\vec{E} \cdot d\vec{A} = \iiint_\Omega \rho_f \ dV - \oint \vec{P} \cdot d\vec{A}$$
Applying the divergence theorem and combining the right side integrals:
$$\oint \epsilon_0\vec{E} \cdot d\vec{A} = \iiint_\Omega \rho_f - \nabla \cdot \vec{P} \ dV $$
Finally, ##-\nabla \cdot \vec{P}## is what we call the bound charge density ##\rho_b##, so the integrand on the right side is ##\rho = \rho_f + \rho_b##, or the total charge density including both free and bound charges, so we're left with $$\oint \vec{E} \cdot d\vec{A} = \frac{1}{\epsilon_0}\iiint_\Omega \rho \ dV $$
What is bound charge density? Well, consider a conducting place in an electric field. Because of the applied external field, the atoms in the material form small dipoles, each of which cancels out the field from the adjacent dipole, except on the edges of the material. This surface charge constitutes the bound charge density. This, by the way, demonstrates the importance of always being aware of explicitly what it is that your variables represent when applying equations.