Import CER file into NTAuth Store on Windows Server 2003

KB 317541 (Event ID 8 is logged in the Application log): http://support.microsoft.com/kb/317541 has the answer.

Cause: This behavior can occur if the Update Root Certificates component is turned on and the computer cannot connect to the Windows Update server on the Internet. The Update Root Certificates component automatically updates trusted root-certificate authorities from the Microsoft Update server at regular intervals.

Resolution: To resolve this behavior, you must connect to the Internet or turn off the Update Root Certificates component. To turn off the Update Root Certificates component, follow these steps:

1. In Control Panel, double-click Add/Remove Programs.
2. Click Add/Remove Windows Components.
3. Click to clear the Update Root Certificates check box, and then continue with the Windows Components Wizard.

The only thing that springs to mind that might be a generic issue rather than one specific to ThirdPartyApplication(tm) is that if the machine it is reading the file from does not have sufficient client access licenses. With server editions it depends how you have the licensing configured and what licenses you have (for XP there is a fixed limit of 10 concurrent connections if I remember rightly). I have seen connections get "hung" in some cases on XP, such that no new file sharing connections can be opened until XP is restarted, though I have never seen this on a server edition, so the old faithful solution of restarting Windows may be a quick-fix work-around until you can find a more permanent solution.

If it isn't a licensing issue then you should probably contact the creators of that third party application as your first resort: they may be aware of a possible issue and already know how to fix or work around it.

ps. for questions such as this, it is helpful to specify the exact Windows version+variant that is installed on both machines, and what the third party application in question actually is - then if by chance someone else has hit the exact same problem previously you might get a quicker (more accurate) answer.