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You could try loading up a different browser in the background for your tests if it's an issue. What I do sometimes is run Firefox with TMN's automatic speed test and then use Chrome for browsing. Then you don't have to worry about closing the browser on accident and you can clear your cookies without an issue. I just ran a few auto tests with extraID and it's working fine so it's probably because your clearing your cookies thoughout the day.

Having an MTU above 1500 may actually result in a slow-down if path discovery isn't working correctly and your packets get fragmented. That being said, if everything is working, the MTU should auto-adjust.