When the domain mapping plugin is used with wordpress, but no domain is selected as primary for the blog (ie the domain.com/blogname is the primary by default) selectors that rely on the blog name all read domain.com where the should be domain.com/blogname or name of blog.
If that sounds hard to follow, do this to reproduce:
1. Create a wordpress 3. multisite install using subfolders.
2. Create sub sites subsite1 and subsite2
3. Install domain mapping plugin, map subsite1 to subsite1.domain.com and subsite2 to subsite2.domain.com but uncheck primary on each.
4. Install plugin "Add Clone Sites for WPMU (batch)" from http://wordpress.org/extend/plugins/add-cloned-sites-for-wpmu-batch/installation/ and network activate it
5. Go to Sites > Add Cloned Sites in the wordpress backend, click the dropdown list "Select the template site which will be cloned" and note that they are all the same name and impossible to distinguish between!
Note that this is not specific to this plugin, using the Blog Diamond Multisite Widgets bloglist widget will generate a list that contains the same main site over and over again when using the domain mapping plugin, this is not an issue when the domain mapping plugin is not used or is an earlier version (not sure when this issue was introduced though).