We have seen this as well when doing the following.....

Adding new device and in the name field you put the fully qualified name. Then when you do the test connectivity, it appends the second domain naming structure on the end of it. We have gotten around it by entering just the dns name, not the fully qualified name, and then it is correct when it appends the fully qualified name after connecting to it.

It is a little different case, but same type of results. don't know if that helps or not, but you are not alone in seeing this type of activity.