For any other world than the default world specificied in server.properties, the following issues occur up until the latest version:

• Chests do not generate in desert temples and villages but they work in dungeons; their content lies dropped as items on the floor
• Minecart with chests generates twice on the same spot in mineshafts
• Cave spider spawners are not being generated, only the surrounding cobwebs are

It might be helpful to know that dungeons work perfectly regardless of world. The issue was introduced with the 2.7.0 release, 2.6.4 worked just fine. Further investigation has shown that this is the commit responsible for breaking the above: 705d169#diff-de0477a76fa5a4e1f3240b8502955459fc8dd9c1a5cce2ad6fc5642136b51ef9