2 Year Route still possible after successful appeal?

I am a British citizen.
My partner, who entered the UK on a 1 year student visa, applied for FLR as my Unmarried Partner in May 2012. In Feb 2013, it was refused. In Jul 2013, we won the Appeal (within the rules).
According to the current Guidance, those who APPLIED for FLR PRIOR to 9th July 2012, will be considered against the old rules and eligible for the 2 year route.

My partner's timeline
pre 2011 - we were living together for 2 years in another country.
June 2011 - Entry into UK as student.
May 2012 - Application for FLR as Unmarried Partner
Feb 2013 - Refusal Letter
July 2013 - Appeal won (within rules)
Resident Permit is date December 2013 and has a duration of 2.5 years.

It is clear in the Appeal Judge's ruling that she ruled there was an error in the UKBA decision and hence our original application was ruled to have been Within the rules at the time.

However, the 2.5 years suggests that the Home Office granted the FLR outside of those rules.

According to the basic facts and guidance - i.e. the date we applied for the original Unmarried Partner Visa, we should be eligible for the 2 year route to ILR.
But the length of the Residency Permit concerns me.

Any advice please?

You should be covered under the transitional provision in A277A.

I believe it is worth a fight.