Hello and thanks you for using Just Answer. You must get Form 5498 reporting the rollover from the IRA custodian. When you received Form 5498 from the IRA custodian, send a copy of the form and all records of the rollover to the address listed on the IRS letter you received with a statement that you received the pension's check on 12/01/2008 and completed the rollover on 01/28/2009.
No, it's mandatory that the rollover occurs when you received the distribution and within 60 days reinvests the assets in another eligible retirement plan.
The IRA custodian should have sent Form 5498 to you and the IRS which is the reason the IRS have sent you a notice for underreported income in the amount of the distribution.