The difference between Cat5(e) and Cat 6 will not be obvious for home users but is certainly noticeable in large business deployments. Cat5 and 5e are capable of providing 100MHz whereas Cat6 is rated to 250MHz, assuming it is installed to specifications. In addition to the increased frequency, Cat6 is has much greater protection against crosstalk and system noise which is far more important to many sysadmins.

Previously we benefited from the honour system in place, many Cat 5 cables actually met the Cat 5e specification but it seems that this is not the case with Cat 6. Hack a Day has heard word through a cable provider that Fluke noticed that 80% of the Cat 6 tested with their equipment does not meet specification, in many cases it does not even meet Cat 5e specs. Since a Fluke line tester capable of analyzing network cabling to this degree of accuracy costs north of $10,000 not all companies are going to have their networks fully tested for compliance. This may be why you are seeing odd behaviour on your network.

"So they did some research and purchased a Fluke certification tester for a measly 12,000 US dollars. While they were purchasing the device, they ran across an interesting tidbit in the fluke knowledge base. Fluke said that 80% of the consumer Cat 6 cables they tested didn’t begin to meet the Cat 6 specification."

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