This happened in LR3.7 and continued when catalog was imported into LR4:
I import by date in these folders: year/month/date
So imports today would go into the 2012 folder - March subfolder - March 30 subfolder
But recently this happens: At the import screen, the correct sub-folder (March 30) is chosen on the right side with the correct number of images. But when the import is executed and I look at my folder structure on the left side in Library mode, the March 30 subfolder has appeared twice--once where it should be as as a subfolder to March, and once above March, and sometimes above all of 2012. The March 30 subfolder of March is listed as empty. The folder in the wrong place has the images. If I try to move the images to the proper folder, it says the images are already there! If I look at the system finder, indeed the image files are where they are supposed to be, and the phantom folder does not exist.
If I right click on the folder where the images are and select update folder location it won't let me choose the correct folder. Sorry if this is confusing....it's driving me crazy. In many years with LR this has not happened before
P.S. By starting a new test catalog in LR 4, I cannot replicate the problem.. is the catalog corrupt?
Try exporting affected images as catalog, removing affected folders from
main catalog, then importing back.