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I'll appologize now for the fact that some of these questions probably seem trivial, but maybe they'll help.
I’m assuming you’ve already pinged the server and that comes out OK. How bad is the latency?
It sounds stupid, but verify the client and server are on the same release of Intralink (I know, just like the tech asking if a computer is plugged in
Have you tried running a client locally on the server?
Can you run a ptcstatus.bat from a client?
Have you tried using the fully-qualified name of the server when entering the server location for the client?
Is the Intralink DSMU running correctly on the server?