I'm not sure how else to describe this. It's not terribly frequent but occasionally the game will lag for a second when it needs to play a sound or pop up a text flyaway. I suspect this has to do something with reading information from the hard disk. I thought maybe it was an issue with a mod I was playing but the issue also occurs playing the vanilla game with no mods loaded.
I thought it was related to my PC but I recently got a brand new PC with a new instance of Windows. Just transplanted the steam drive from my old PC though, so if it's an issue relating to disk reads I guess the drive may still be responsible.