From the UKBA website http://www.ukba.homeoffice.gov.uk/vi...ormset%28m%29/
If we gave you permission to remain in the UK as an unmarried or same-sex partner and are now applying to settle here as the husband, wife or civil partner of the same person, your 2-year qualifying period started on whichever is the later of these two dates:
- the date when we gave you permission to remain as an unmarried or same-sex partner; or
- the date when you arrived in the UK.
It looks like when you applied for FLR, that is when your permission to remain was granted and therefore the two year period starts then.
When you applied FLR, did they put a visa in your passport, if so, when is that visa valid till?