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The only time you will see cat6 show improvement over cat5 is when you are nearing the bandwidth limit of the cat5 (probably cat5e) cable. The cat5 cable you are using to connect to your router will handle 5 to 10 times the bandwidth that your cable modem or dsl will provide. So cat6 cable will not increase performance for you(I am literally surprised that best buy support staff actually answered a networking question correctly, I have horrible luck with best buy techs not having any clue what they themselves or I am talking about).
Make sure you have the latest firmware on your router! Lynksys routers have been prone to performance decreasing firmware bugs (hence the firmware hacks available all over the internet). As mentioned traceroute is your friend! More than likely all your problems are outside of your local network. traceroute will show you the exact hops that are slowing you down.
** No offense to any best buy employees who may be members, I speak of my personal experience only
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