Apple Mail (v6.6, Mac OSX v10.8.5) mixes up mail threads - why, and what can I do?

Question

Dear community,
I am having a weird synchronisation problem. My Mail (v6.6) on my MacBook Air (Mac OSX v10.8.5) mixes up random email threads after I read emails on my iPhone (5C).
E. g. there is an email thread with Frank. Frank writes a new email that I read on my iPhone. Shortly after, I open Mail on my MacBook, so that Frank’s email is downloaded there as well, displayed as "read" and added to the existing thread with Frank. However, although still being named "Frank", showing the current date and reference, in fact it is an email of Fritz from two years ago, having nothing at all to do with the thread with Frank.
Synchronising with the iPhone with USB has no effect, although the emails remain correctly displayed on the iPhone. On my MacBook’s Mail, the email from Fritz keeps to exist a second time at the time and place where it is supposed to be. Frank's email that has been replaced incorrectly, seems to be lost.
I don’t have to explain how unfortunate such random email shuffling is. I shall be thankful for any support and hints. Many thanks,
Ray Taras

Answer 1

Make a temporary, backup copy (if you don't already have a backup copy) of the library and try the following:
1 - delete the iPhoto preference file, com.apple.iPhoto.plist, that resides in your
     User/Home()/Library/ Preferences folder.
2 - delete iPhoto's cache file, Cache.db, that is located in your
     User/Home()/Library/Caches/com.apple.iPhoto folder. 
Click to view full size
3 - launch iPhoto and try again.
NOTE: If you're moved your library from its default location in your Home/Pictures folder you will have to point iPhoto to its new location when you next open iPhoto by holding down the Option key when launching iPhoto.  You'll also have to reset the iPhoto's various preferences.