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What's the order you're trying to patch in? To get it to work properly, I had to install each patch sequentially from the base 3.2, to get to 3.2.3.MJH
Did you (or can you) enable Hyperthreading? This helped enormously with ours which have about 450 devices each (although we still upgraded both our boxes to 2 CPU's). Also, be sure not to login to CW on the server console, as a lot of java componen...