The knock, or "kack" as I call it is the exhaust loading up with unburnt fuel. It will happen if you don't "clean it out" after warming the bike up after you first start it too. (Get the bike on the pipe for a few gears)
I had to go a little leaner on my jetting on my 300 to get that to stop. I also noticed that if I am in the woods all day, I could use leaner overall jetting vs. riding a motocross track as I also do on my 300.
Unfortunately I cannot suggest jetting changes for your 250 specifically, but I can say that you may want to go leaner.
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'10 EC300 -- very happy 
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