I just noticed this bug myself.  Not sure if I just didn't notice before (hard to imagine), or if it is new.  I noticed Windows had an automatic update last night, so perhaps it is related?
 
In my case, it has nothing to do with project complexity.  I have a single tempo and one track (two takes).  Increasing ASIO buffers has no effect.  Fortunately this is not critical, but very odd and annoying.  

It looks like a bug that came with X3D.

I too have an Nvidia card (GTX 560ti) and my now time marker completely freezes anytime I move the mouse while the mouse is in the TV.  The now time marker freezes in all windows (I have two monitors) but only when the mouse cursor is moved within the TV.  Moving the mouse in PRV or anywhere else doesn't seem to affect the now time marker.
 
If I move my mouse in a circle (continuous movement) in the TV, the now time marker will sit still for as long as I continue to move the mouse.  As soon as I stop the mouse movement, the now time marker plays back as expected.  Playback of the song is not interrupted at all...just the now time marker movement.

CakeAlexS
Mind you I'm on 314.22 (old nVidea drivers), which seems to be more stable for me (latest drivers BSOD my system periodically!).

I have exactly the same problem while moving the mouse around the tracks lane area. All the graphical animated items stops to refresh correctly during the moving. I tested the behaviour on 2 different machines with respectively a GTX 460 (same driver as yours 314.22 and BTW it seems the very latest driver corrected the issue we have with all the newer version than 314 ;) ) and an ATI HD 5790. Same issue. Pay attention that I noticed that the problem only arises when there are numbers of tracks/lanes/clips. If you start a new project with just some tracks the problem is not noticeable, then it progressively becomes more and more choppy as you add elements to the project.
 
Hope this could help in the investigation

Question/suggestion for everyone experiencing this issue. Do you have Aim Assist enabled? Try disabling it and/or setting a larger snap resolution. I see this problem when Aim Assist is on and snap is off or set to a fine resolution where the Aim Assist line has to update at a high rate.

brundlefly
Question/suggestion for everyone experiencing this issue. Do you have Aim Assist enabled? Try disabling it and/or setting a larger snap resolution. I see this problem when Aim Assist is on and snap is off or set to a fine resolution where the Aim Assist line has to update at a high rate.

Thanks for your suggestion.
Yes I have the Aim Assist on, but this just make the problem worse and it is not the cause of the problem in itself. In the sense that in fact being a problem of refresh everything that make the GUI heavier raises the problem faster, but if you have a project with many clips or tracks, moving the mouse will completely freeze the interface until you stop to move it around, so activate or deactivate the aim assist would make you gain only the possibility of having a couple of more tracks before arriving at the worst frame rate situation. At least this is in my case.

I'm experiencing these problems too. I had to switch to X1 to get any work done. Affected PRV editing as well as grabbing clip ends on top of aim assist lag. Called tech support about it last week.... For fun you might highlight all clips, right click, then Associated audio files, recompute picture, see if the behavior changes any. Like I said, just for 'fun'. :) My graphics card is a NVIDIAGeForce GTS 250M.

Anyway it is confirmed as a bug, probably the worst one in x3D at the moment. I haven't tried it with my steps, but it being triggered by aim assist makes total sense, there seems to be a lot of half baked behaviours with it. If it is aim assist triggering it, it gives us some sort of workaround.

I dont know if this will help shed any light but I just went from X1 to X3, no other changes, no patches installed yet.  Opened a small 8.5 project, six audio tracks (24/96), no midi, no tempo changes.  I'm seeing the jumpy 'now time' for the first time ever with Sonar.  Playback is normal.

I'm glad someone else is noticing this. I have also encountered a situation where certain plugins (Machfive 3) will essentially cause SONAR's meters and GUI elements to completely stop refreshing. I suspect that it is the Nvidia video card. I never saw this issue when I used to use AMD (ATI) video cards. I reported it a while back to both Cakewalk and MOTU, but nothing was ever done. I've just learned to minimize those plugins to get the GUI back to being usable.
 
-e.B