Biome/Terrian Generation Issue with Worlds from old versions of Minecraft

A world I created in a version of Minecraft before 1.6, has weird biome and terrain generation when loaded in Minecraft 1.6. Beyond areas already explored before the patch, any terrain abruptly 'stops' and is seemingly replaced by new terrain with a wholly different biome. For example, a tall mountain that existed in the world would be 'cut off' completely, resulting in a sheer drop at a given line. Alternately an ocean would 'cut off' in exactly the same way and no matter the depth instant land would result; land of a completely different biome. There also appears to be a 'step down' between the old generated terrain and the new; the new terrain is usually one block lower and this does not cause water to flow across, even though it is at a higher elevation than the new terrain below it.

Lighting and physics are not consistent across the abrupt boundary in biomes and terrain. For example if a 'cut off' mountain contained a sealed pitch dark cave, this cave would remain completely dark even when the new superimposed terrain exposed it to light. Also, water does not flow at all across the boundary and instead creates a 'wall' of water that appears to be flowing downwards but never crosses the boundary. Water and light usually do not appear to move across the boundary unless acted upon by the player. For example mining out a block from a pitch dark cave from the newly generated side would cause the light effect to now work correctly and illuminate the cave. Placing blocks into the water 'walls' and then mining them out will also cause the water to flow correctly, but only at that single location, all other water still appears to be inexplicably blocked from flowing. One exception to this situation is water sources that have momentum, usually those coming from underground out of the 'cut off' mountains; these appear to correctly flow across the boundary.

I have never seen the elevation of the newly created terrain be higher than that of old terrain. New terrain is either Swamp or endless Ocean in my experience.

This issue impairs the function of worlds created in earlier versions of Minecraft, especially for players desiring persistent realistic worlds for Survival mode, though the issues occurs with older worlds in both Survival and Creative modes