You need to make sure the maps your changing are appropriate for the tools client...
Either convert the maps or inside the source files for the tools change the following before you compile in vmapextractor and mapextractor:
1) add custom patch name onto the source it's easy to see where these are listed.
2) change the version number of the game that's allowed - this might mean you don't have to convert the maps.
You will see an area where the build versions are for the game in the tools source files just add yours here.
You don't need to touch the other tools as they build off of what we changed.