Thanks for your question
Sadly you have no grounds to appeal under ESC A19 as you did not contact HMRC regarding your tax position, for them then to fail to act.
Its true that they failed to work the P11d sent to them by July 2008, but this in itself are not sufficient grounds to appeal.
When you received your P60 and P11d did you not query why the company benefits differed ? Please advise whether you took any action at all regarding these company benefits.
HMRC can now ask for the tax return to be completed, as it may be there are further considerations, however, have they advised why you now need to complete a self assessment tax return, due to the fact they have already issued a P800 calculation? Are you a higher rate taxpayer (the income and the benefits in excess of £39825 for the year) as this may be the reason.
Getting tax is a three way responsibility, yours, the employer and HMRC, and it would seem that both you failed to act, HMRC just failed to act as soon as they could have and you did nothing to query the position. And as you quite rightly say it is unfair, but this again is not grounds for appeal.
However I would try and establish when the employer sent in the P11d , was it on time, did you have a company car, did the employer advise HMRC that you had this company car, from the start, or did you have a change of company car during 2007/2008 that the employer failed to advise HMRC on... I am trying to see if there are grounds to hold the employer liable for the tax bill.