It seems like the MeshMerger script from the wiki itself was causing this trouble. On fourth thought and investigation it seems like copying of triangles and vertices is kind of buggy in the script, so finally I also saw some lonesome vertices flowing in the world after combining. Therefore it might not be the best idea to use that script at all.
Nevertheless, the CombineChildren script from the Standard Assets turned out to be a much better basis to work with. I've rewritten parts of it now to suit my needs, which basically is generating the combined static geometry in the editor and being able to generate lightmaps for this as well. Works like a charm!
I've seen this topic multiple times in the community without a real solution, so it might be a good idea to have a script ready for this. No big adjustment, but I hope it helps some people out there. Here it is, use it as you wish.
CombineChildrenAdvanced.cs Usage: Place this anywhere in your project and attach it to the parent gameObject containing the other meshes to be combined. Basically it delivers the very same feature as the standard CombineChildren script, yet it needs to be executed in the editor. By default it'll automatically generate the lightmapping UVs for the combined geometry. If you don't want this to happen, either use the CombineChildren.cs from the Standard Assets, or uncheck the corresponding checkbox. If you want to split geometry up again, just use the corresponding button. It'll reset everything accordingly.
Code:
using UnityEngine;
using System.Collections;
/*
Attach this script as a parent to some game objects. Then by using the corresponding controls you may generate combined meshes (with lightmapping UVs).
This is useful as a performance optimization since it is faster to render one big mesh than many small meshes. See the docs on graphics performance optimization for more info.
Different materials will cause multiple meshes to be created, thus it is useful to share as many textures/material as you can.
NOTE: Using multiple materials may break things due to lightmapping generation. So lightmapping UVs as well as splitting the combined geometry is not supported.
Workaround: Create hierarchies in which the children only have exactly one material.
*/
[AddComponentMenu("Mad Vulture Games/Combine Children 1.5")]
Note: While the script still gives you the opportunity to use it with meshes with multiple materials (which will effectively generate multiple new gameObjects), this is not supported in this version, you might get errors. If you need that, feel free to build that yourself or let me know, shouldn't be hard to add.