HMRC has confirmed that penalties for late filing can be appealed if a taxpayer registered for the online filing services on or before 31 January; and filed the return as soon as possible after 31 January.
A penalty notice will issue because it is now too late to stop HMRC's systems issuing one. The penalty must be appealed in writing, but as long the taxpayer meets the conditions described above, HMRC will accept this as a reasonable excuse for filing late, and the penalty will be withdrawn.
HMRC has also acknowledged an issue with the information displayed on the View Account page of the online filing system affecting customers and agents who have filed 2007/08 returns. The View Account page may show an incorrect figure for the tax owed. The amount shown on the first screen is the total amount owed.
To view the amount becoming due for payment, select the figure shown as 'will become due'. This will display a correct statement of the amounts and when they are due.
For further details on the self assessment deadline see here