I have two files whose content is identical except for the order in which I placed the assertions: in one file, the assertions are placed in the reverse order of the other.
What could be the reason for this difference?
SMT solvers implement DPLL(T) algorithm, which is a combination of (a variant of) the DPLL procedure and decision procedures.
Performance of DPLL is heavily affected by the choice of variables for branching. There are the cases of which the running time is constant or exponential depending on variable selection.
If the two formulas are logically equivalent (you need to double-check), then I think the only possibility is that, the different order in the two formulas leads to different order in variable selection, which eventually leads to difference in performance.