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I don't see anything in options that could be handicapping the cookies, so I don't know what's up.
Does that account for what you are seeing - a number of the sites you visit regularly are placing boatloads of cookies (near the limit of 20 per server), or you visit a boatload of sites that place cookies.
As far as I can make out, scanning it, there is a limit on both the maximum number of cookies (300) and the number of cookies per server (20).
I think this behaviour will change in version 1.0, but is still present in 0.9.