CGI Timeout

do you have any specifics in the IIS logs?
C:\WINDOWS\System32\LogFiles\
or even more logging
http://support.microsoft.com/kb/324279

maybe a typo in the location?

What actually can cause CGI Timeout when clicking on a link which will download an .exe file ?

not sure
http://supportline.microfocus.com/mf_kb_display.asp?kbnumber=22222&show

Problem
The following error message is displayed in the web browser before the CGI is completed:
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CGI Timeout
The specified CGI application exceeded the allowed time for processing. The server has deleted the process.
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The above error occurs after 5 minutes.

 
Resolution
The CGI timeout setting (not Connection Timeout) in Microsoft IIS server is defaulted to 300 seconds (or 5 minutes). If the CGI takes more than 5 minutes to complete, IIS will return the CGI Timeout error to the user's web browser and delete the process from the web server.

Here are the steps to change the CGI timeout setting in IIS 5.0 of Windows 2000 and IIS 5.1 of Windows XP:
1. Open Internet Information Services (Control Panel > Administrative Tools)
2. Expand Machine_Name (local computer)
3. Right-click on Web Sites
4. Click on Properties
5. Click on the Home Directory tab
6. Click on the Configuration button
7. Click on the Process Options tab from the Application Configuration window
8. Increase the number of seconds from CGI script timeout field
9. Click on the Apply button
10. Click on the OK button
11. Click on the OK button

It is now different the way to change the CGI timeout in IIS 6.0 of Windows 2003 Server. Actually, the Process Options tab is no longer available from the Application Configuration window.

Before you can change this setting, here are few things you need to do first:
1. Open Internet Information Services (Control Panel > Administrative Tools)
2. Right-click on Machine_Name (local computer)
3. Click on Properties
4. Check the "Enable Direct Metabase Edit" options
5. Click on the OK button
6. Close Internet Information Services
7. Install the IIS 6.0 Resource Kit Tools - this is available from the Microsoft Download Center at http://www.microsoft.com/downloads

Here now the steps to change the CGI timeout setting:
1. Open Metabase Explorer from Start > All Programs > IIS Resources > Metabase Explorer
2. Expand Machine_Name (local computer)
3. Go to LM/WESVC
4. Look for ID 6033 or CGITimeout under the Name column
5. Double-click the entry to edit its properties
6. Change the value
7. Click on the Apply button
8. Click on the OK button

For further readings, the IIS 6.0 online documentation is available at the Microsoft Windows Server 2003 TechCenter site. This can be accessed directly at http://www.microsoft.com/technet/prodtechnol/WindowsServer2003/Library/IIS. The keyword or topic that addresses this issue is "Metabase". CGITimeout is a Metabase property. You will find everything about Metabase at IIS 6.0 Documentation > IIS 6.0 Technical Reference > Working with the Metabase (IIS 6.0).