If memory serves correctly users where able to login using either email or username in a standard login form until a few days ago. The site uses zoo_visitor latest version and has been updated to EE 2.6.1 to handle the new zoo visitor forgotten password form.
Login using username/password on both Zoo and EE login forms is fine. Try using email and error:
The existing username and/or password you submitted are not valid
Any ideas? Is this because of the updates? My next port o' call is stepping through the php, thought id ask here first.