The main problem is actually the list of modules. It seems to reorder them now and again and that causes lots of conflicts when new modules are added. It's hard to fix these merge because you have to really pay attention to what is going on.
Because it uses an INI style format for identifying files in the project, if we both happen to add a new modules between commits, it causes a big problem because the counts are correct but we'll have to hand edit and increase the count and add the conflicting file by hand during the merge.