For TTX to show a difference of only a few bucks is really of no concern, as it really makes no difference in the tax liability anyway. I've since cases similar to this where say they start using TTX in the 15th year of having the rental. Prior to the year they started using TTX the 4562 for that prior year would show $1 more or $1 less than what TTX calculates for the current year. That's fine. Just leave it alone and press on with life.
But if you've got something like say, a difference of a few hundred dollars or so, then something entered in the program is not in agreement with what's on that prior year's 4562 is all.
I've seen people use the acquision date as the in-service date, and that can cause the first year convention to be off, which throws it off for all years following. The error I see most often is where they use the "Cost (net of land)" figure as the total "cost", and that will definitely throw the math off every time.
Another less common (but frequent enough) mistake I see is where they've entered the property as domestic rental property when it's foreign, and vice-versa.
