When using the Re-create feature the map won't be an exact copy if the version you're using and the version used to generate don't match.

Recreation steps:
-Generate a map in 1.3.2
-Re-create the map in version 1.4.2 with the exact same settings
-Note that this world is similar but has differences, the most obvious of which are 1.4.2 features

Desired results:
-The world would be generated using the 1.3.2 generating engine since that is the engine originally used to generate the map. Currently it appears to only copy the seed.