In the description of the instanton Floer homology of a surface times a circle due to Mu~{n}oz, we compute the nilpotency degree of the endomorphism $u^2-64$. We then compute the framed instanton homology of a surface times a circle with non-trivial bundle, which is closely related to the kernel of $u^2-64$. We discuss these results in the context of the moduli space of stable rank two holomorphic bundles with fixed odd determinant over a Riemann surface.