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This is a classic problem that is indeed very difficult to diagnose. Many of the most pernicious problems in networking are simple to resolve ONCE YOU KNOW WHAT IT IS. But finding the problem is incredibly time consuming and frustrating.
I can offer you three things:
1. My white paper on Traffic and Everything That Looks Like Traffic http://searchnetworking.techtarget.com/whitepaper/1,289194,sid7_gci903796,00.html – it might have an idea or two that will help you isolate this "traffic-like" behavior.
2. An off-the-cuff diagnosis – based on the very little you have described in your question, I can imagine a couple of likely sources for your problem. I would first look for an MTU black hole – check the end-to-end path MTU if you know how. If you don't, check our Web site for the MTU white paper http://www.apparentNetworks.com/wp/.
Next I would suspect a problem with a cable or interface on one of the routers or switches on that path.
If possible, query every device in the suspect path and look for unusually high error rates or corruptions. If you find high error rates, change the cable and/or interface to see if there is any effect. If you find nothing (or don't have SNMP access or login to the devices), depending on whether you are working with optics or copper, try reseating cards and replacing cables everywhere on the path.
3. Try appareNet – this is a blatant plug for our technology that I won't apologize for. In this case it is the right answer. I would fearlessly bet money that it would diagnose this problem in under an hour.
Of course, the problem may rest with an ISP who is providing the WAN link (you don't mention who owns/operates the WAN link). In which case, answer three) is the only way I know to look into your ISP's networks.
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