The Simplified Method is a way to disperse your "Basis" (after-tax contributions) in the pension over the course of some time frame, so that only some of the basis is returned tax-free to the taxpayer each year. Note that this process is for a qualified plan (like a 401(k)). Non-qualified plans do the return of basis upfront, so if there was enough basis in the plan, you could easily have a year in which the entire distribution is tax-free.
Since we have no idea what your plan is (or it is even a plan versus an IRA), nor any of your entries, we can only speculate on the difference. So what do you have, what is on the 1099-R, and what answers did you supply TurboTax in the 1099-R interview?
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