Mail should mark it read when just clicking on it, if not there is corrupyion, bad spotlight index, or bad Mial index.
Safe Boot from the HD, (holding Shift key down at startup), does the problem occur in Safe Mode?
Safe mode attempts to repair Disks & clears lots of caches, so if Safe Mode works try again in regular boot.
If you have no POP accounts & they’re all IMAP accounts then in Mail’s Mailbox menu choose Rebuild.
How to rebuild the Spotlight index on your Mac
If searching your Mac doesn’t return expected results, rebuilding the Spotlight index might help.
- Choose Apple menu () > System Preferences, then click Spotlight.
- Click the Privacy tab.
- Drag the folder or disk that you want to index again to the list of locations that Spotlight is prevented from searching. Or click the Add (+) button and select the folder or disk to add.
- To add an item to the Privacy tab, you must have ownership permissions for that item. To learn about permissions, choose Help from the Finder menu bar, then search for “permissions.”
- From the same list of locations, select the folder or disk that you just added. Then click the Remove (–) button to remove it from the list.
- Quit System Preferences. Spotlight will reindex the contents of the folder or disk.
If still not working...
Manually Rebuilding Spotlight via Terminal
If the aforementioned Spotlight control panel approach doesn’t spur a reindexation of the drive, you may need to initiate it manually through the command line. Open Terminal and use the following command string to do so:
sudo mdutil -E /
This basically asks for temporary super user status, which is why Terminal may ask you for your password (it may not if you’ve used a sudo command recently or are already logged in as a super user or root. The command asks the unix tool mdutil to reindex the spotlight database for everything on the computer, including external drives, mounted disk images, etc. To re-index only for a specific drive, use the /Volumes path. For example, for an external drive named “MiniMe,” the command would look like this:
sudo mdutil -i on /
Rebuilding a drive index can take a long time, so be prepared to wait whether you do it through the System Preference panel or the command line.
If still need be…
Open Terminal and run each of these one at a time
/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -kill -r -domain local -domain system -domain user
sudo /System/Library/Frameworks/CoreServices.framework/Frameworks/LaunchServices.framework/Support/lsregister -kill -seed -lint -r -f -v -dump -domain local -domain system -domain user -domain network
killall Dock
sudo mdutil -E /
sudo mdutil -i on /
Rebuilding a drive index can take a long time, so be prepared to wait whether you do it through the System Preference panel or the command line.
