Interesting post this morning.
Two clients (more to follow?) where we successfully appealed against late filing penalties (because 2011 Returns should never have been issued in the first place) have received £580 penalties for late filing. These have been calculated at 58 days x £10 per day from 3 months after the paper return filing deadline.
It seems to me that HMRC have somehow logged the Returns as "received" when they accepted that Returns shouldn't have been issued and their systems have picked this up as being a late paper return - originally due in 31/10/11.
I'm now left having to waste more (unchargeable) time fending off clients who are being pusued for a hefty penalty they don't owe and get HMRC to cancel this and, maybe, apologise to the client.
It beggars belief - roll on retirement.