If you start a new game (create a new profile first, so you don't overwrite any quick or auto saves from your current game), or load an old save that was fine before, do you still have this problem?
Are you shutting down all non-essential programs (especially anti-virus) before starting the game? Firewalls have caused conflicts (generally on loading screens, though) and overlays from graphics tweaking/monitoring programs or chat programs have also caused issues.
Do you have any delays when using the mouse and keyboard UI?
In the Game section of the options, try lowering the vibration slider to zero. There is no vibration during conversations, but it is worth a shot.
Another person had a performance problem when using a controller to sneak or target certain skills, which were fine with the mouse and keyboard. The same thing happened in another game, but was fixed by disabling vibration. In the EE lowering the vibration didn't help, but disabling force feedback in the X360ce emulator they were using for their non-Xbox controller did.
If you switch the game to a windowed display mode, does that make any difference?