LR 1.2 Import Function - Shows Previously Imported Directories

I have 40,000 pictures I am trying to import into lightroom. I have 1500 left to go. The process I used has been:
1. File:Import Photos from Disk
2. I then select the main directory that has every photo I have taken or scanned. The directory structure is MAIN DIRECTORY/YEAR/EVENT.
LR scans all directories and runs its' comparison.
3. The "problem with Importing Files" dialog box appears to let me know the following photos will not be imported because they already exist in catalog.
a. Best I can tell it generally gets most of the files that have already been imported correct.
5. I select IMPORT and I then get the dialog box import photos.
a. It shows I have 44 folders left to import.
b. At least 20 of them (I am guestimating) have already been imported.
c. When I select a directory, for example. /Thanksgiving 2003, those photos appear correctly in the preview section.
d. I know these have been imported already and are in my catalog. For giggles, I enter my keywords 2003,Thanksgiving and select IMPORT.
e. I am using "IMPORT FILES AT THEIR CURRENT LOCATION", BTW.
6. Sure enough, the dialog box appears:
a. Import Results | Some import operations were not performed | The files already exist in the catalog (21).
6. I want to NOT view those 20 directories whenever I run the IMPORT function.
a. Also, there are a few directies that had 100 photos imported. The IMPORT CATALOG COMPARISON shows that there is 1 photo in a directory that hasn't been imported. Of course, it has, because when I try to import the one remainind item, is clearly shows as IN LIBRARY.
HERE IS THE IMPORTANT ISSUES, most of the directories are correctly being imported and then removed from the initial scan. I had hundreds of directories that are disappearing from the catalog comparison correctly. It is just these 20 or so that will not go away.
Needless to say, I would like to run import and have NO FILES or DIRECTORIES to import when I am completed this project.

Jao, as a general rule I always want to see exported jpegs or tiffs in LR library. My ideal is to not have to use the file browser in Windows to manage files. I want to know if I have jpeg or tiff versions of a raw file. Otherwise I might end up creating identical jpegs, when I receive a request for a particular file. Since my jpegs are created from raw files adjusted in LR's develop module, I have been considering deleting the jpegs after sending them to the client who requested them, that way I don't waste hard drive space on files that I can easily recreate. Even in this case, I would like to see them in LR, so that I can delete them after sending them to the client.
I create tiffs for two purposes. One is to edit in PS, which automatically gets recognized by LR. But some times I create tiffs that are used in assembling an HDR file. I want to see these in LR, otherwise I need to open the Windows file browser and navigate to the folder to see the tiffs.
I prefer to work in a single program so in general I would like LR to be able to recognize other file types such as Acrobat or InDesign files. The more the better as far as I am concerned. LR could have a preference that would allow turning off the display of other file types, so users who don't want this will not see them.

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