This is just a hunch, but could you try doing a repair operation on the .NET platform? All of our networking is handled in that level and I'm thinking something might be getting hung up in there. Repairing .NET may likely take down anything using it while the repair is happening though so you'll probably want to schedule for after hours. Let me know what it finds :)
Kyle Kerst
IT Coordinator
SmarterTools Inc.
www.smartertools.com