The account that runs the ASP.NET process must be given permission to use the PKCS12-format key that was imported to the local machine store.
The name of the the ASP.NET account is typically "NETWORK SERVICE" (although it may use another name on your system).
http://www.microsoft.com/downloads/details.aspx?familyid=c42e27ac-3409-40e9-8667-c748e422833f
The tool installs to the C:\Program Files\Windows Resource Kits\Tools directory by default; winhttpcertcfg.exe is the name of the executable.
WinHttpCertCfg -g -c LOCAL_MACHINE\MY -s "Endeca" -a "NETWORK SERVICE"
Microsoft (R) WinHTTP Certificate Configuration Tool Copyright (C) Microsoft Corporation 2001. Matching certificate: E=support@endeca.com CN=Endeca User O=Endeca Technologies C=US Granting private key access for account: NT AUTHORITY\NETWORK SERVICE