It's the date of the INITIAL visa application for the first settlement visa to move to the UK that should matter.
As she applied for her fiance visa before JUly 9th 2012, she SHOULD have been given a 24-month FLR(M).
HOWEVER, it looks like she has been given a 30-month FLR(M), which means she is on the new rules and has been issued the wrong visa... this should have been checked and clarified at your in-person appointment and you needed to have made sure she was processed under the old rules, because they may have assumed she was under the new rules.
If her FLR(M) visa is valid for 30 months, I'm not sure what she can do because she is not allowed to apply for ILR until 28 days before the expiry date of the visa - she should qualify for ILR after 2 years, but she hasn't been granted an old rules FLR(M) which would allow her to do so.