It's been SO long since I've played the game. I just recall not really seeing it while I was playing it and it's kind of like 'recalling being confused at the time' by this stuff.
To not continue off topic for much longer, it seems there are a few things as you've said. I'm not sure I'd say it means they are together in an actual relationship though, or if it is, it's a secret one or one that maybe happened in the past and didn't last. Her line about Balthier having different methods seems to imply he tried to court her at one point in the past. But then, if they were together now, why would Vaan let his friend send love letters and flowers to Fran if she's with Balthier. Doesn't exactly add up.
However, it adds an interesting part to their relationship I never thought of before. [/derailing thread]
EDIT: I know we aren't suppose to go off topic like this so if anyone did want to reply maybe a mod could split it, and if not, then don't worry about it.