Sync between Lightroom 3 and Photoshop CS5

Question

I continue to have problems with updating the Lightroom 3 catalog.  Yesterday I highlighted 4 icons of CR2 files and opened them in CS5 to do a photomerge. I saved the result as a psd file then as a jpeg file in the same directory that the CR2 files were stored. On returning to Lightroom, those files were not in the catalog so I went ahead and imported them into the catalog.  No luck--still no icons.  The original files had been tagged with a keyword so I highlighted the keyword and then clicked the right arrow next to the keyword.  The icons then appeared but after another minor edit in Photoshop they disappeared. I wanted to copy the jpeg to Flickr and eventually did so but it took multiple steps of closing Lightroom, choosing the keyword, filtering the files before I got it done.
I am relatively new to Lightroom but worked extensively in PSE 6 and earlier versions and do not remember having anywhere like the problems I have experienced with Lightroom.  My impression is that Lightroom is designed for a specific workflow, not to serve as a reliable database to keep file versions and edits easily accessible.

Answer 1

I finally figured out where the edited files went--to a higher level subdirectory.  Lightroom was not happy with my directory structure which had the pictures in subdirectories three levels below the /User/xxx/Pictures directory in Windows 7. Importing images always required choosing the correct subdirectory and apparently this problem carried over when I sent images to Photoshop and saved changed versions.  I did find the specific option to send to Photoshop to create a panorama and that process worked correctly to place the panorama in the original directory.
Anyway, having struggled with this mess I spent quite a bit of time moving images to a higher level subdirectory.  Do you have any insight into why Lightroom chokes on what worked perfectly well with Photoshop Elements?