Library creating a new duplicate folder structure

I am using 2.0 on a Mac. Recently I moved all my data files including photos and lightroom catalogs from an external to an internal drive on my MacPro and renamed the new drive with the same name as the external and changed the external name and it became a backup. Lightroom continued to work just fine, seeing all the images with no problem. If I do a "Show in Finder" it shows me them on the internal HD. However, when I import a new image or even import an image or folder that has previously been imported, LR brings it in within a new folder structure that uses the same hard drive name.
My actual hard drive folder structure for my data drive is something like HardDriveName/Graphics/Airshows/image.jpg with all my images in a Graphics folder and within that a series of folders and subfolders.
Previously if I imported a new folder, LR would show HardDriveName/NewFolder and I have several folders of imported images with that structure. It did not include the /Graphics folder because I never imported the entire Graphics folder. Now however, after importing a folder, LR created a new folder structure in the Library with a duplicate of the HardDriveName and it included /Graphics.
I went to the first folder structure and picked a small folder and made a change to an image to darken it a great deal. Then I imported the folder all over again and it imported it to the new folder structure but the dark version was not visible. I DO have automatically write xmp data checked.
If I right click on any image from either folder structure LR shows me the image within the same hard drive where my original are found.
I don't want to have two folder structures and apparently if I re-import all my images LR doesn't see the xmp data. I tried to tell RM to read the xmp data from the image I had changed after it came into the new folder but it did not show up. If I manually tell LR to Save Metadata to File for a folder in my original structure and then go to the same folder in the new structure that LR is showing and tell it to read metadata it will show up in the new folder. I have a folder with 32,000+ images and thousands of other images.
I would like LR to continue to bring images into my "old" folder structure but that may not be possible. Any help?
Interestingly I have more than one data drive. This problem does not seem to be happening with my other data drive that I also swapped to an internal configuration.
I put a pic of my folder structure at http://www.pbase.com/santa/image/101246417 to illustrate the issue. My harddrive name shows as Brandon.
I spoke too soon. LR seems to be creating a new folder structure for two of my three hard drives and adding images properly to one of my three hard drives. All three were new drives with the names changed to match the old drives.

yes I did update camera raw. I think LR 2.0 asked for that. I did a search on "duplicate" and found no answer to my problem. Anyone with a link to any useful information?

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