My basic assumption was always that the following events occured;
Original timeline
Leene is kidnapped by Yakra, Frog reaches the Cathedral and rescues her
Marle's Initial Disappearance
When the King finds her (Marle/Nadia), the search is called off. Before Crono intervenes, Frog, either unknowning of "the Queen" being returned OR not believing it to be her (Her pin missing and her unusual behavior being suggestions she is not the original) goes to the Cathedral, finds that Leene is in fact still being held by Yakra, and rescues her. This becomes the initial timeline until Crono arrives (As explained in the next part). Marle dies in the 600 A.D. timeline, but this has only a nominal effect on time, because, unless she tells everyone exactly what's going on (And everyone believes her), this is a ridiculous idea and nothing would happen to her. Leene would still have her offspring, who would continue reproducing until Marle is in fact born again.
Crono's Arrival in 600 A.D.
Crono arrives between the time that "Leene" (Marle/Nadia) is found and Frog rescues Leene at Cathedral. Isn't it coincidental that, even though Leene is safe, Frog is at Cathedral, still thinking something to be out of whack?
Crono and Lucca then assist Frog with restoring history, and go about completely screwing it up by doing everything possibly to mess with our heads.
To me, this was always the most logical.
(I bumped this because I thought it was still relevant conversation and this might help the speculation a bit)