Lightroom 3 and Photoshop CS6 problem when editing

Hi,
I have just upgraded to Photoshop CS6 and now when I 'edit in Photoshop CS6' from lightroom and save it, the image doesn't appear next to the original RAW file as it did before. Now lightroom creates its own folder with the edited files in.
For example, I edited a RAW file from a folder called Bissoe valley from Lightroom and saved it. When I go back to Lightroom the edited image is not next to the original file but in a seperate folder called 'Bissoe valley'. I then try to drag the edited image back into the original 'Bissoe valley folder with the original RAW file and it says 'the file already exists at the destination'
I appologise if this has already been asked. I'm guessing I need to buy Lightroom 4 because of incompatibility issues? It wouldn't surprise me if this is the case.
Thanks in advance for any help.

Victoria....you are a legend!
You can see here lightroom has created folders identically named to the folder which the original files belong to (coco, Harriet, Bissoe and independent assignment)
The really confusing part is that when I look in the original folder outside of Lightroom, the saved Tiff image is there next to the original.
I think I will try uninstalling ps cs6 and go back to cs5 to see if it solves the problem and take it from there....

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