Lightroom :: Photos No Longer Stacking After Photoshop Edit

I have Lightroom 4 and Photoshop CS6 running on a Mac. I have the box checked to stack edited with originals.
 
I recently moved all of my photos to a an external Raid 1 drive - I did this within Lightroom, so that Lightroom knew where everything was. Everything seemed to be fine.
 
Today, I realized that after going to Photoshop and coming back into Lightroom, my photos are not stacking. Not only are they not stacking, but according to Lightroom they are not in the same folder, even though they are.
 
I am not working from a collection, I am working from the actual folder structure on the drive. If I go to photoshop, edit, save and come back, when it returns to Lightroom, where normally the new edited Tiff would pop up - now it returns a black screen, saying "no photo selected". If I go to the library module, the screen is still black. If I go the top of Lightroom and click on "All Photographs" the tiff file is there next to the picture. However, it is not stacked. If I try to stack it, it says that it can't stack photos that are stored in different folders.
 
I don't know where Lightroom is putting this Tiff file. The folder that I was editing from had 20 photos in it. I went into photoshop, came back with a tiff, and there are still only 20 photos in the folder, yet if I go up to all photos, it is there, so Lightroom put it somewhere.
 
When I go look at my external hard drive, the tiff file is there. It is right next the raw. In the same folder. So, it seems that Photoshop is putting it back in the right folder, but Lightroom is not.