HMRC offers a 1% discount for those registering for the Flat Rate Scheme as an incentive. The 1% discount you get within the first year of Flat rate registration begins from the day you register for VAT, not the day you become Flat rate registered.
If you pay VAT to HMRC based on when the business pays expenses and receives payments from clients (also known as cash basis for VAT), the 1% discount applies to clients payments received in the first year, rather than dates invoices are raised.
Example - X Limited
X Limited registered for VAT on 14/05/2016, so the 1% discount will apply to all payment received from clients from that date to 13/05/2017. The VAT rate then reverts to the sector specific rate or the Limited Cost Trader rate of 16.5% if applicable.