I've had these issues as well. Though, I have an old 2.6 GHz AMD Athalon 64 X2 5000+ processor.
I have a very capable GPU and six gigs of ram as well. Win 7 64 bit OS
These micro lags happen every five to twenty minutes of play. They last about 3-5 seconds with a minor break in the stall and then stall again for 1 or 2 seconds until the game resumes.
During these periods I also clip through walls though luckily I take no fall damage.