In that case I hate to be the bearer of bad news, but as a service organisation you probably should have been paying VAT at a 16.5% flat rate, not 11%.
The 11% only applies if you're not a "limited cost trader".
If you spend less than 2% of the value of your sales on goods (not services) over the period your VAT return relates to, then you can't use your 11% rate and have to use 16.5%.
HMRC brought in the rules because people were using the FRS to pay less in VAT, whereas it was brought in, really, to ease the administrative burden of doing VAT returns where you record VAT on both income and costs.
Rather than just change everyone's percentages to a more appropriate level, they brought in the limited cost trader rules so you have to do a calculation each quarter to determine whether your spending is higher or lower than 2% of sales (hint - it is very unlikely to be, unless you go through LOADS of stationery).
None of our clients had costs of more than 2%, so would have had to apply the 16.5% rate. For comparison, the flat rate scheme calculation method is based on gross sales, so VAT on a £1,200 invoice (£1,000 + 20% VAT) is the equivalent of 16.667%. On a £1,200 invoice you'd have to pay over £198 of VAT, when you'd charged £200 - so a "profit" of £2.
Alternatively if you're on the standard rate of VAT you'd pay over £200, but you'd be able to reclaim VAT on any relevant business expenses. Paying your accountant alone would be sufficient to make it financially beneficial to not be on the Flat Rate Scheme.
I have to say I think you've been very poorly advised if you weren't made aware of the Limited Cost Trader rules.