I don't know I think it kind of makes sense.
I suppose the reason someone gets a +2 flanking bonus to hit is because his enemy is distracted by two threatening opponents on opposite sides, right?
However, an invisible flanker doesn't really provide as much a distraction as a visible one.
The PHB says that combat is not static.
pg 122.
Even if a character's figure is just standing there on the tabletop like a piece of lead, you can be sure that if some orc with a battleaxe attacks the character, she is weaving, dodging and even threatening the orc with a weapon to keep the orc a little worried for his own hide
A O B
A= fighter w/ imp. invis.
B=visible rogue
O= flanked opponent
IMO, the invisible fighter would gain only the bonuses for invisibility. The rogue would not be able to sneak attack nor get a flanking if he or the opponent cannot see the fighter. why?
if the reason for the flanking bonus is bec. of distraction on the opponent's part, then the invis. fighter does not count as distraction.
Why? well since he is invisible, we can effectively consider him off the map for purposes of perception. the only enemy O can see is B and thus he focuses most of his attentions on B. Even if A is constantly harassing O with attacks and even if A threatens O, O is not sure of A's true position or the exact nature of the attacks upon him.
to conclude, O can see only one enemy and he cannot do anything meaningful against A (unless he can see invis or has a really good spot score). So he concetrates on B. Unlike the normal conditions for flanking, his attention is not divided and thus he is not distracted. Thus, B is not eligible to gain the +2 bonus to hit nor the sneak attack.