If you can see this discrepancy by looking at the top of the mt-check.cgi results:
To correct this behavior, so that the Current Working Directory and MT home directories match, you would need to create a new "virtual directory" under IIS which points to the physical directory where the Movable Type CGI files are located (i.e., the "MT home directory" mt-check.cgi reports).
For example, you might create the virtual directory /mtdir, /mt-admin, or similar to point to the physical directory C:\Inetpub\yourdir\mt\.
For more information, please see the following Knowledge Base article (but do not download and install theBootstrap.pm file mentioned in the article):
http://www.sixapart.com/movabletype/kb/known/cgi_error_on_iis.htmlAfter creating a virtual directory as described above, try browsing to the mt-check.cgi using the URL to the virtual directory just created, such as http://domain.com/mtdir/mt-check.cgi, and make sure that the "Current working directory" and "MT home directory" match. If so, then try browsing to the mt.cgi script using the URL directory, such as http://domain.com/mtdir/mt-check.cgi, and see whether you still encounter this issue.
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