I agree with @AmeliesUncle; it appears as if your tax preparer calculated the deprecation deduction using the wrong period.
You can try filing Form 3115. However, it certainly seems as if your tax preparer entered the correct recovery period (27.5 years) on Form 4562 but then calculated the deduction over 40 years which, essentially, amounts to a math error for which Form 3315 cannot be used to ameliorate.
