IFilter 9 64-bit deletes files and moves them into idividual folders

Our fire department scanned thousands of documents using Adobe Capture and stored them on a Windows Server 2008 R2. We then installed iFilter 9 64-bit so Windows Search could make these documents searchable. The second day iFilter was installed I noticed some unknown folders in the root of c: with names such as A9R2f4-115f67e8. By the third day these had grown to thousands of folders, each with one PDF document in it. I recognized the files as the ones that had be captured with Adobe Capture and checked their original location and found the files missing. It appeared that in indexing the files Windows Search with iFilter was moving each file into an individual folder. I removed iFilter and the problem stopped. Luckily I had a backup and was able to restore the files to their original location.
Months later I installed a new server at a different location. Thinking this was possible a conflict with another program or service on the original server I copied the adobe documents onto this new and clean server and installed iFilter 9 64-bit. Again, the first day things look fine but on the second day the folders once again started showing up in the root of C:, again I removed iFilter 9 and the problem went away.
This would appear to be a bug in the program since it has happened to two server, one a brand new Dell R710 with nothing on it except the server software and Adobe iFilter and the PDF files that were captured using Adobe Capture. I have called Adobe and I was told they do not provide support for iFilter other than this forum. If anyone has any suggestions I would really appreciate the help.

Erwin,
I was not able to systematically examine this issue, because it occurred on a production system and, of course, I uninstalled the Adobe iFilters as soon as I read that they may delete pdf files. Before the uninstallation I noticed the AR9 folders appearing on c:\ and moved them from time to time to another folder. Using the search function inside this folder, I found that all files were present in duplicate at least. I concluded, that after moving the AR9 folders they were recreated containing the same files. Consequently, these files cannot have been deleted. Searching for the origin of these files I found that they were part of pdf portfolios, therefore my conclusion that they are part of the indexing mechanism of the portfolios. What I have not done (and what I am not going to do since it is a production system) is to fill a folder with pdfs and track what is happening to the files.
In case of my server, I think that the iFilters did not delete any files. Of course I cannot say what happens on other systems. I am definitely not going to reinstall the iFilters before knowing what they a really doing to the files.
Not sure if this is of much help
Michael

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I was not able to systematically examine this issue, because it occurred on a production system and, of course, I uninstalled the Adobe iFilters as soon as I read that they may delete pdf files. Before the uninstallation I noticed the AR9 folders appearing on c:\ and moved them from time to time to another folder. Using the search function inside this folder, I found that all files were present in duplicate at least. I concluded, that after moving the AR9 folders they were recreated containing the same files. Consequently, these files cannot have been deleted. Searching for the origin of these files I found that they were part of pdf portfolios, therefore my conclusion that they are part of the indexing mechanism of the portfolios. What I have not done (and what I am not going to do since it is a production system) is to fill a folder with pdfs and track what is happening to the files.
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IFilter 9 64-bit deletes files and moves them into idividual folders

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