zones.php isn't used anymore, zones are queried from the database directly now. There is no longer a need to change that silly file when zones are added or changed. I let that system slip by far too long!
You can download the newest version from SVN (using a SVN client) that has this functionality, which was part of an overhaul to get the editor to support instances. Or, I was planning on posting the newest version for direct download tomorrow after I get a couple more small things in. The new version will be at least revision 172.
As for your other problem... Grab the newest version first and try to add a new NPC to your zone and see what happens. The original NPC you created may not show up if the NPCID you chose is out of the zone's range (One day I'll add the ability to toggle how the editor places NPCs into zones.) If a new NPC still does not get added, reply with the id, zoneidnumber, and version of the new zone you created.
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