http://www.sureai.de/development/tutorials/skyrim-creation-kit-version-control/
I've written the WhoCanMerge bit also in the SkyrimEditorPrefs.ini, like recommended above in comment number 12 - in the tutorial this not clearly mentioned. Don't know if it works, when it's only written into SkyrimEditor.ini, so be aware of that.
The absence of that feature is the source of most of the bugs, like I mentioned above, so it's very advisible to activate it and make use of it.

(ok, you can, but it wont work.....).