I am resolved my apparent issue. I was trying different scenarios of Roth conversion amounts together with various regular IRA deductions to offset the extra tax due to the conversion. When the IRA deductions are fully deductible, everything is fine and the MAGI (line 12 in IRA Deduction Worksheet) comes out as it should be. When the deductions are only partly deductible, it is a little bit trickier but everything is consistent.
As for the oddity I was referring to in my previous post, it is not real: the IRA deduction that you subtract from Total Income to get to the AGI is then added back to the AGI to get MAGI, so the amounts are canceling out, meaning they are not really there in the calculations.
Thanks for those interested in the discussion; it was a good sounding board for me to write about it.
