Here is an example:
In X13 of "Faisceaux amples sur les schemas en groupes", Raynaud provides an example of a group scheme G -> S in chacteristic 2 where
- S is a local regular scheme of dimension 2.
- G -> S is smooth, separated and quasi-compact.
- The fibers of G ->S are affine and the generic fiber is connected.
such that G -> S is not quasi-projective.
Therefore, the classifying stack BG has affine stabilizers but does not have a quasi-affine diagonal.
On the other hand, in VII 2.2, Raynaud proves that if G -> S is a smooth, finitely presented group scheme such that
- S is normal.
- G -> S has connected fibers.
- The maximal fibers are affine.
then G -> S is quasi-affine.
Question: Is the above statement true if (2) is weakened to require that the number of connected components over a fiber s \in S be prime the characteristic of the residue field k(s)?
Of course, one would really like to know if the statement is true if G->S is not necessarily flat so that one could apply it to the inertia stack.
On a related note, Raynaud also provides an example in VII3 of a smooth quasi-affine group scheme G -> A^2 over a field k with connected fibers but which is not affine. The classifying stack BG gives an example of stack with affine and connected stabilizers but with non-affine inertia stack. In the example of a scheme with non-affine diagonal, the inertia is of course affine. It's also easy to provide examples of non-affine group schemes with affine but non-connected fibers (eg. the group scheme obtained by removing the non-identity element over the origin from Z/2Z -> A^2).