I had this problem, and partly found it to be the USB hard drive on which the clips were stored, an external drive. Having bought a couple of small drives (80gb) and fitted them internally the situation improved significantly, but did not entirely disapear. A jump to a 4gb RAM, 1gb graphics RAM, Quad core processor with SATA hard drives the problem has gone altogether, so I would say, irrespective of file type as I've used FLV's, MOV's, AVI, HDV and MOD files with no difference, that it's a hardware issue.
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