I have a similiar problem as well, I already made a thread about it, but I lag only in certain programs.
Everything else is running smooth, but I noticed you lag in Google Chrome as well, I lag there too, along with Divx player (web and desktop player), MSN (which forced me to downoad Pidgin to even log in), Quicktime player, and possibly other programs I have yet to use.
My computer is also custom built and only 3 months old, with updated bios and everything.
Don't meant to double post, just wanted to let you know you're not alone.