What are you doing in transferring your wort from your kettle to fermenter?
I use whirlfloc, then after cooling get a good whirlpool going (helps with aeration as well) and let it sit for 15 minutes. Then I siphon from the kettle into the fermenter, leaving the coalesced trub behind. Remember that's what the whirlfloc is going to do - grab onto proteins and sink them to the bottom.
Quaker City Brewing Co.
On Tap: Brewerytown Bitter
In the Works: Poplar St. Pale Ale, Boathouse Brown Ale, Philadelphia Porter