Line 4a on the 1040 should show $9,000 and so should line 4b (note: other amounts may be included if you had other IRA distributions, so the $9,000 is the minimum). ALSO NOTE: because of the weird IRS instructions, the amount in 4a may be zero or blank. As long as the $9,000 shows up in 4b, this is correct.
Line 4c should show the $9,000 401(k) distribution. Line 4d show not show the $9,000 because a rollover is not taxable (again, if you had other pension or annuity distributions, they will be added to these two lines).
Only the IRA's $9,000 should appear in line 8b, your Adjusted Gross Income.
If 4d includes the $9,000, then you need to return to the 1099-R interview and make sure that you indicated that this event was a rollover.
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