Time separators blinks inconsistently
Some thoughts about how to track this down:


In System Preferences > Language &amp; Text > Region, do you have any unusual settings?  (Some of these influence the formatting of the clock... from the video, you have the same settings as me, but I wonder if you have anything unusual here that perhaps Apple haven't tested too well?)
Is there any pattern to the absence / presence of the separators?  Eg, from your video, I see they are absent at 46, 47 and 48 seconds: is this true for every minute?  (In which case, perhaps the cause of this might be some logic bug in the code that determines whether the separators should be shown for a given number of seconds.)
I believe the SystemUIServer process controls many of the icons on the menu bar, including the clock.  If you use Activity Monitor to quit it, it will quickly relaunch, but you'll get some insight into what that process is doing.


Some thoughts:


Is SystemUIServer perhaps using a lot of CPU?
Try removing any non-Apple menu bar icons for the moment (by quitting the appropriate apps), and see if the issue goes away.  I suggest this because: even if SystemUIServer isn't using much CPU (and the system CPU load is low), I suspect that if one of the menu icons it controls blocks (that is: performs some system call which doesn't immediately return, perhaps because it is waiting for some data), then the updates of the clock might be paused.


After discussion below, seems that unfortunately none of this has helped to isolate the issue.  The only remaining possibility I can think of is that you've run into an Apple bug... in which case, you might consider reporting it at bugreport.apple.com.  (I have a paid developer account, but I believe that isn't required to report bugs there.)