same here, although the difference ain't so dramatic, I guess it has something to do with slight variations in thermal paste coverage and surface of contact with the HSF...
i did not have that on the stock cooler though,,,,
i guess this is becasue it is a tower cooler, that means that the core closer to the fan(which is on one side) will get more of the colder air first.....man this sucks...maybe i should return it...although it is so damn cool.....
i think i will try and reinstall this again, although it is a major pain.....