I seem to be experiencing the same problem with a POP account that's setup to use global folders (Edit -> Account settings -> [POP account name] -> Server Settings -> Advanced). Any incoming mail triggers a notification bubble but fails to change the color of the messaging menu icon.
However, if I use a separate inbox for the account, then new messages do trigger the desired color change.
I seem to be experiencing the same problem with a POP account that's setup to use global folders (Edit -> Account settings -> [POP account name] -> Server Settings -> Advanced). Any incoming mail triggers a notification bubble but fails to change the color of the messaging menu icon.
However, if I use a separate inbox for the account, then new messages do trigger the desired color change.