Lightroom not finding DNG files in the folder

Question

I am using Lightroom 2.5.  My library includes a folder with approximately 5000 images which is located on an external hard drive as is my Lightroom catalog.  I use the external dive because it is part of a RAID 1 array to backup my images. 
My problem began when I used Lightroom to convert the 600 RAW files in the folder to DNG files.  Prior to the conversion, the library tab showed that there were 5000 files in the folder.  After the conversion, the library tab shows that there are only 4400 files.  The DNG files are actually there but Lightroom will not recognize them.  I can use windows explorer to see them and that there are 5000 files in the directory. 
I have tried to synchronize the folder, but it did not help.  I have also tried to write metadata to the files to make sure that was not the problem and it was no help.  As a test, I also copied the directory to my local hard drive and imported that into Lightroom.  That folder has the correct 5000 images, but of course non of the ratings that I had applied to the 5000 files to organize them so the local folder is useless.
Can anyone suggest a means of convincing Lightroom that it should recognize the missing DNG files that are actually there?
Thank you.

Answer 1

John,
Thank you for your suggestions.  I do have filters off. 
I started up Lightroom today and again, the Folders tab only showed that the folder had 600 files which corresponds to the missing 600 DNG files.  Furthermore, in the grid view, only the 600 DNG files were appearing.  But, after a minute and without my input, Lightroom loaded up the 4400 JPEG images into the grid and the DNG files disappeared both from the file count and the grid view.
When I look at the All Photographs folder in grid view, I can find the missing DNG files so they are in the All Photographs folder. 
I did as you suggested and I optimized the catalogue.  Now when I launch Lightroom, I see the missing 600 DNG files in the grid view and the file count for the folder.  But that only lasts a few seconds before the 4400 JPEGS appear and the DNG files disappear.  So the optimization made the loading faster as it should, but did not help Lightroom to find the DNG files.
Now when I try to synchronize the folder, It does show that there are 600 files to be added.  However, synchronization does not help and DNG files are still missing.
I can see the DNG files in a folder called “Already in Catalog” from when I tried to synchronize the original folder.  After optimizing the catalog, I told Lightroom to write metadata for the DNG files.  Once I did that, some of the missing DNG files did appear in the grid view of the original folder (but not all of the 600 missing files).  However, the library still only shows 4400 files in the folder. 
One last oddity. When I change the sort to “user order” from “capture time”, I see only the 600 missing DNG files in the grid view.  The 4400 JPEG files are gone.  But when I change the sort back to capture time, the JPEG files and the few DNG files are there again and most of the DNG files are gone.
This bugginess is only occurring on the external drive.  The same files saved to the local hard drive all appear in the file count and the grid view.
Thank you.