It has to do with how many of the old zones have been revamped. Now, if you wanted to use the newer versions of zones like Freeport, Southro, etc, you would need to make adjustments so that things are setup to use the new zone layout. Otherwise, you have spawns trying to move around in a zone that is a different shape than the one you are in and weird stuff will happen. Also, many races were updated so rats would use new models and other races use different models, so you would have to adjust those races to the new ones.
This thread might help a bit as well:
http://www.eqemulator.net/forums/showthread.php?t=28026