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There are unread mails in my Gmail account, but GmailAssistant does not seem to detect them. When I right-click on the tray icon and select "Check Mail Now", GmailAssistant logs into my account without error, but returns with zero unread mails.
The problem is probably caused by IMAP folder name discrepancies under some regional settings.
If you are using labels for your "notify" setting, make sure they are correct. Labels should appear as they do in the web interface of Gmail.
In the web interface of Gmail, go to Settings > General > Language. Note the current setting, and change it to "English (US)".