I spent time a while back looking at email addresses as usernames, and other scenarios. Things should work better throughout in 1.3, but some users (dots in username, email addresses in usernames) probably need to set define( ‘BP_ENABLE_USERNAME_COMPATIBILITY_MODE’, true ).
I’d prefer this to be smarter and automatic for BuddyPress, but I don’t think anything more work will happen in the 1.3 release, for this issue specifically.