For the royalties, are you entering them using the O&G screen, rather than directly on Sch E? OK O&G is something that Lacerte is usually pretty good at.

For the farm, are all of your deduction items coded OK, rather than KS?

The IRA distribution is allocated taxpayer by taxpayer, so if you have a married couple, the allocation won't be based on overall earned income.

Edit: I can't reproduce this problem; I'm even getting the OK depletion adjustment automatically and the IRA deduction matches my manual calculation. The only thing I can think of is that your individual line-item entries aren't coded to the correct state, because that causes all sorts of issues.