Frame skips in deus ex (comes out looking like microstutters even though you're on a single card) are unavoidable on certain hardware. I have the exact same problem and the only method that I found to alleviate it to where it is absent from the game 90% of the time, was to turn up the pre-rendered frames in nvcp from default 3, to 5. This did more to smooth the game than anything else, but also some of the stutters seemed to be related to a poor implementation of DOF, which you can disable or set to a lower value in the in-game options.
Few things have ever actually pissed me off regarding gaming more than watching a perfectly good Deus Ex game literally be crippled by something as dumb as an inexplicable microstutter.
I did try playing Deus Ex: HR, but it was on my older video card (8400GS, yeah, not the type to game with...)
Although the graphics looked really outdated, the microstutter was just too much..
I have yet to start playing the game.