I rolled over a 401K into an IRA, and it is showing as (non-taxable) income. As a result, some of my deductions are not allowable. THis does not make sense because it was not income, it just changed accounts. What am I doing wrong?

A non-taxable 401(k) rollover should only show on the 1040 form line 4d as a 0 (zero) amount and noting in line 4c (taxable).     That does not get added to AGI and has no effect on anything else on your tax return.

What deduction seems to be reduced?

You need to enter the ROLLOVER code = "G" from your 1099-R.