The script outputs that the count_visible is True, that's quite strange...
Can you please test the current UM version from trunk?
- go to http://bazaar.launchpad.net/~mitya57/unity-mail/unity-mail/view/head:/unity-mail
- download that file
- run "pkill -f unity-mail" to stop running instances
- cd to your downloads directory
- run the downloaded file using "python3 ./unity-mail"
Also, the script reports that you have option "Hide count when it's zero" enabled — is that true? Can you please attach your ~/.config/unity-mail.conf file?
Thanks in advance!