Yes, prenex normal forms are not unique for a given FO formula, and,
correspondingly, Skolemizations are not unique. A simpler example for the
same "scope escape" I think you are trying to show is the formula ∃xAx →
∃yBy, with prenex forms ∀x∃y (Ax → By) and ∃y∀x (Ax → By), and respective
skolemizations ∀x (¬ Ax ∨ Bf(x)) and ∀x (¬ Ax ∨ B a), with a a constant.
Now, the pertinent question is whether the non-equivalence of those
formulae matters for your particular problem. If it does, perhaps
Skolemization is not the best tool for you: Skolemization is a process
designed to preserve satisfiability of formulae, sometimes at the expense
of equivalence.
(and in any case, it is a good exercise to see why distinct skolemizations
of a single formula are equisatisfiable, if only on the examples above)