Can you provide more detail on what you did when you got the "domain already exists" message?
Also, can you provide some info on your install? UTL, domain you are mapping, etc.?
I'm a savvy developer, so I can easily dig in and help figure this out. but I just don't know where to start with this plugin.
There have been no substantial changes in WP that would affect this plugin since WP 3.4. The issue is something with your install, conflict with another plugin, etc.