R – Unable to browse some pdfs and docs

I have a web site that uses Microsoft Indexing Service to index and query a directory that holds various documents of type pdf, rtf, mht, and doc. The indexing and querying works well (for the most part); however, some files will load while others will not.

This is a Windows Server 2003 box running the site using IIS 6.

The indexed directory is a sub directory off of the site's root directory (i.e. http://my.domain.com/files/).

The file paths are accurate in the URL; however, I can only access some of the files of each file type. The files that I cannot access give a 404 File Not Found. I am able to open all files via windows explorer;however, attempting to open them via a browser over http is hit and miss.

Has anyone experienced this issue and know how to resolve it? Anyone have any idea why I could access some files but not others? Does anyone have any recommendations on what to look into to try this (i.e. does owner matter or something like that?)?

EDIT:
Here is the Request and Response Headers for a bad file:

GET /files/file1.pdf HTTP/1.1
Accept: image/gif, image/jpeg, image/pjpeg, image/pjpeg, application/x-shockwave-flash, application/xaml+xml, application/vnd.ms-xpsdocument, application/x-ms-xbap, application/x-ms-application, application/x-silverlight, application/vnd.ms-excel, application/vnd.ms-powerpoint, application/msword, /
Accept-Language: en-us
User-Agent: Mozilla/4.0 (compatible; MSIE 8.0; Windows NT 5.1; Trident/4.0; .NET CLR 1.1.4322; .NET CLR 2.0.50727; .NET CLR 3.0.04506.30; .NET CLR 3.0.04506.590; .NET CLR 3.0.04506.648; .NET CLR 3.5.21022; .NET CLR 3.0.4506.2152; .NET CLR 3.5.30729)
Accept-Encoding: gzip, deflate
Proxy-Connection: Keep-Alive
Host: my.domain.com

HTTP/1.1 404 Not Found
Content-Length: 1635
Content-Type: text/html
Server: Microsoft-IIS/6.0
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Date: Mon, 01 Jun 2009 15:38:54 GMT
[typical 404 page markup excluded]

Here is the Request/Response headers for the good file:

GET /files/file2.pdf HTTP/1.1
Accept: image/gif, image/jpeg, image/pjpeg, image/pjpeg, application/x-shockwave-flash, application/xaml+xml, application/vnd.ms-xpsdocument, application/x-ms-xbap, application/x-ms-application, application/x-silverlight, application/vnd.ms-excel, application/vnd.ms-powerpoint, application/msword, /
Accept-Language: en-us
User-Agent: Mozilla/4.0 (compatible; MSIE 8.0; Windows NT 5.1; Trident/4.0; .NET CLR 1.1.4322; .NET CLR 2.0.50727; .NET CLR 3.0.04506.30; .NET CLR 3.0.04506.590; .NET CLR 3.0.04506.648; .NET CLR 3.5.21022; .NET CLR 3.0.4506.2152; .NET CLR 3.5.30729)
Accept-Encoding: gzip, deflate
Proxy-Connection: Keep-Alive
Host: my.domain.com

HTTP/1.1 200 OK
Content-Length: 352464
Content-Type: application/pdf
Last-Modified: Tue, 13 Jan 2009 15:27:35 GMT
Accept-Ranges: bytes
ETag: "74ccc5759375c91:2a47"
Server: Microsoft-IIS/6.0
X-Powered-By: ASP.NET
Date: Mon, 01 Jun 2009 15:50:33 GMT