Losing Dex bonus to AC and flat-footedness are different things
Losing Dex bonus is generally less severe, and flat-footed usually includes it. Flat-footed also precludes "reactions" such as immediate actions, attacks of opportunity and such (like, for example, maybe, free action to make an opposed grapple check to resist being grappled, provided, an opposed check is a free action for both combatants). Lost Dex bonus, on the other hand, enables sneak attacks and such. Note, Flatflat-footed by itself doesn't.
Invisibility and Rules Compendium (RC)
It seems, impact of "invisible" condition is changed by RC. Prior to RC, it was that you are denied Dex bonus to AC when someone invisible strikes you. RC adds this in a Hide skill section:
If you’re successfully hidden with respect to another creature, that creature is flat-footed with respect to you. That creature treats you as if you were invisible.
Passage quoted has nothing to say about if "that creature" has already acted or not. It may be argued both ways if the phrase works another way around (like, if you are invisible, you are hidden, so the target is flat-footed for you). I think, it is logical, you can't react to something, happening all out of a sudden, but maybe it's just me.
I should also note, that RC authority is controversial. While it is probably intended for the later to be absolute, it seems WotC have failed to make it so, formally.