LR4 saving CS6 edit in a separate LR Ghost folder

Ladies & Gents,
If anyone has an answer to my problem I would appreciate it. For the record I have searched forums here and other places on the web and have found similar problems but not quite the same.
When I right click > edit in CS6 go to photo shop after completing my work I click "save" (not save as) the photo is saved back to light room showing as a separate photo but in a separate folder in LR. In finder the file saves back to the same folder as the original file. The file should show as a separate image but the folder should be the same. This was working fine until the last few days.
Interestingly if I try to drag the file in LR4 from the new "Ghost folder" to the original LR recognizes that the image is already in the same directory in finder and will not allow the move.
Needless to say this is infuriating, I can move the file in finder delete the record in LR and then re-import back to the correct folder. This work around is annoying and I would rather be moving on and editing the next image! Have also tried a reinstall of LR with no result.
Has anyone encountered this issue and/or have a solution? I would be grateful.
James.
You can see the "ghost folder" here which is created after clicking CMD-S(Save not save as). Perhaps this started after I created the Iphone Photos folder, I have been unable to think of anything else in my workflow that changed recently.
Version info:
LR 4.4 CS6 V13.0.6 X64 Mac OSX 10.9.3

For anyone who has the same issue I seem to have found my own solution which has worked well.
These were the steps:
1. Shut down LR
2. Move folders in finder to a new location
3. Open LR
4. Right click on moved images folders and select the new folder location
This seems to have solved the Singular and most curious case of the Ghost folders!
James.

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