Short answer: it doesn't.
Long answer: a higher/lower share difficulty does not mean you will be earning more/less, because your expected earnings are independent of the share difficulty: they only depend on your hash rate and on the network difficulty. A higher share difficulty can only increase the variance, but not in a significant way.
Thats why I lost 27% of my WU... I call that significant!
I track my WU, normally it's between 1950 and 2250, with the 1024 blocks I'm getting between 1100 and 1600 so yeah it shows.
A lot of the problems started when that other profit pool started to use middlecoin around new year.
http://www.middlecoin.com/reports/1M3jtksp1upR33SX1VzeCfH5x9fc6zKykR.html
It doubled middlecoins hashrate...
Unlucky, my WU is exactly the same