Numerous reports at Google Groups from several users of Google Reader say that they are unable to manage their friends who maintain a googlemail.com account. To be specific, one member says the following:
I'm having the exact same problem - I have @gmail.com address, she has a @googlemail.com. She can see my shared items on her reader, but I can't find her name among my reader friends.
This is indeed a bug for the time being, and as Google Reader Guide points out, it's currently being investigated.
Forum discussion continues at Google Groups.