As far as the discrepancy between 12,000 B.C. and 600 A.D., I support two previously presented theories: first, that all the continents and islands remaining after Zeal's fall are actually extremely high plateus. After all, who says that North Cape is really all that much higher in altitude than the rest of the Last Village continent? Perhaps North Cape "slopes down" only a slight bit, and the rest of the continent is a high plateu. And the mountain ranges are obviously the tallest in existence at that time. The second theory is that Zeal's fall, rather than producing an upsurge in addition to what would occur as the ice caps melting, actually jumpstarted the process of those ice caps melting. After all, Zeal seemed to be quite the tropical place, and it may have shattered large deposits of ice that were previously connected beneath the ocean. Also, that beam that Lavos fired towards Zeal would logically be a rather hot beam instead of some sub-zero blast of ice, likely melting some ice as well. So the flood at Zeal's fall was actually the end of the ice caps than some prologue to their melting. In that respect, it may be logical to assume that the waters eventually receeded some, being consumed both by the returning life and being more evenly distributed into the weather. As Mr. Oath described, Lavos also may have had some hand in drawing back the waters, as it still needed life to corrupt and consume before it was fully grown.
Now, regarding the north-to-south but. I would suggest NOT taking that globe at the end of the game as the real thing, but still not throwing away the idea of a globe. Who, honestly, is to say that the north pole is north of Guardia and that the south pole is south of Porre? Why can Guardia and Porre not MEET into one single pole, whereas the second pole is somewhere between the two on land - say around the latitude of Zenan Bridge? Just because the game may describe Guardia as "north" and Porre as "south" doesn't mean that, by our definitions, that is how they are. Consider a world that wraps between Guardia and Porre from north to south! Then, when you went north of Guardia, you pass the "North Pole" and wind up heading south through Porre to Guardia, despite the fact that the game makes it appear as though that is heading north! This not only solves the "problem" of the poles, but it also provides some interesting insight to Zenan culture - what do they consider north, and what do they consider south? In fact, do they even consider the points I've mentioned to be the actual poles, or is it somewhere else?
As far as the lack of ice cap deposits, do not automatically assume that the Chrono Trigger world is like ours as far as its status in the solar system is concerned. It does not necessarily spin on an latitudal axis, and it doesn't necessarily spin around the sun at the same time. For all we know, the Chrono Trigger world is the center of the universe, and the sun spins around it! For all we know, the sun is close enough to Chrono Trigger's world to prevent the formation of ice caps, even on the "dark side" of the planet. Just because its inhabitants and geography may be similar to ours doesn't ascertain that its climate is the same, or the way they measure days and years. Rotation around the sun and various seasons may not be a realiable way for the people in Chrono Trigger to count their months and years, leading even further to the suggestion of a different solar system and a different climate. Assumption is, in this case, your worst enemy.
It always occured to me that Lavos had some hand in the disappearance of Magus's castle. I was never sure, but I believe I always had two theories: after all life left the island, Lavos safely brought it under the sea, or when Lavos was almost summoned, the temporal distortions consumed Magus's fortress and those within, banishing them to unknown locations and times (well, unknown for the actual fortress and any remaining Mystics), and at the same time affected the temporal and physical stability of the entire island, causing it to slowly break apart and sink over hundreds of years...
