I believe that the surcharge is calculated as a percentage of the tax due. If there is no tax due (because of a loss) then there should be no surcharge. There are other penalties such as an increased chance of an audit.
Not necessarily true - my annual corporation tax return was allegedly 1 day late last month. Even though the tax had been paid, they charged 5% of the total bill for the year because the paperwork return was late.
Needless to say I kicked up and had the express post receipt. They credited me last week.
Beware
Just to clarify, the surcharge will be a percentage of your liability, not the balance due. 5% if less than 2 months late, otherwise 10%