It's been a while since I've read the books, and I've only read the last book once, but this is the theory I've taken for granted since Moraine first disappeared. If I get names/times wrong, please correct me, but I believe this is a Strong theory.

We have the setup of the situation of Aelfin/Elfin: Lands of Foxes and Snakes. Accessed by Gates. Moiraine suggested that multiple strong forces inside a gate at the same time could cause problems.

Now I don't know if I made an assumption of this, or if it was stated, but I connected two towers to being another access to the realms: The one in the Two Rivers Perrin accessed in a wolf dream to free Faile; the tower (ghenji?) that is on the path to the Blight. Both of these towers have connections to another character we've seen: Slayer, the Luc/Isham merger.

Slayer was formed when Luc and Isam crossed paths going to the blight near this tower. The result was the physical appearance of one with the mental control of the other. In the Dreamworld, this appearance was switched.

Keeping with the towers, it appears Slayer was able to enter the dreamworld "in the flesh" via this tower. This perhaps means that there is joint access to the dreamworld, aelfinn/elfinn lands, and the towers. (Thom saving moiraine)

Now if this relationship exists, the mystery of Cyndane is solved. Moiraine and Lanfear enter through the gate and threaten to rip reality. The Dark One intervenes and allows Lanfear to win the battle, leaving her in a mindtrap at the end.

The hair color of Cyndane is the only thing that doesn't follow, but how difficult is it for a Forsaken to change her appearance?

The result we have is a powerful forsaken that looks like Moiraine (i.e. Rand will trust her), with Lanfear's motives, controlled by Moridin through the mindtrap.

I apologize for not being able to site all these instances and for the mispellings, etc, but I had all of this backed up at one point of time.