It seems that here you are talking about the local exts, i.e. about the sheaves $\underline{Ext}^{i}(A,G_m)$ on $S$. The question is rather tricky actually. The problem is that before we try to answer it, we should first specify what we mean by $\underline{Ext}^{i}(A,G_m)$. We could mean exts in the category of sheaves of abelian groups in the flat topology on $S$, or we could mean exts in the category of commutative group schemes. The latter is not an abelian category so you have to do something before you can define exts. It is possible to do this though. The standard lore is to use Yoneda exts. This is carried out in detail in the LNM 15 book by Oort. Among other things Oort checks that if $S$ is the spectrum of an algebraically closed field, then ext sheaves are all zero for $i \geq 2$.
Over general base schemes the situation is more delicate. First of all there are examples of Larry Breen showing that the ext sheaves in the category of sheaves of abelian groups are strictly larger than the ext sheaves in the category of commutative group schemes. In his thesis
Breen, Lawrence
Extensions of abelian sheaves and Eilenberg-MacLane algebras.
Invent. Math. 9 1969/1970 15--44.
Breen also showed that over a regular noetherian base schemes the global ext groups (in either category) are torsion if $i \geq 2$. Later in
Breen, Lawrence
Un théorème d'annulation pour certains $E{\rm xt}\sp{i}$ de faisceaux abéliens.
Ann. Sci. École Norm. Sup. (4) 8 (1975), no. 3, 339--352.
he strengthened his result to show that the higher exts sheaves are always zero for $1 < i < 2p-1$, where $p$ is a prime which is smaller than the (positive) residue characteristic of any closed point in $S$.
