Won't help much but there isn't an option to turn the now time scroll line off.
 
IIRC correctly there were issues for some with that disappearing in earlier versions X1? X2a? but I haven't seen it mentioned as happening in X3.
 
Have you tried a re-install? Might be time to contact support.

Are there tempo changes in your project?

Are there tempo changes in your project?

Something weird happened to the 'now' playback line in the X2 series when it became an artifact drawn by a separate window process, and not part of the SONAR application window itself. I don't know the technical term for this but you can tell it's different because it started intercepting mouse clicks. I have to move it out of the way when I want re-place a marker in the time ruler, for example.
 
I don't have a solution for you, cparmerlee, but I definitely know what you're talking about. It hasn't happened very often, but when it does, I've found that Now Playback line comes back when I exit SONAR completely and re-open it.

DEF happens here as well.  While not a show stopper by any means it IS a pain in the ass.

I know this thread is six months old, but I just had this happen to an X2 project and I was able to "fix" it.  I have an ancient Juno-60 analog synth that has a weird old midi converter box that controls it.  This midi box theoretically does midi out so you can play the keyboard into the midi interface.  I figured I would do that to work on a synth line.  But the ancient midi converter box was sending some funky constant midi signals into my interface, and I'm not sure whether the midi converter box even works to do midi out anymore.  
 
Anyway, this is a long story to let you know that I sat here for about 30 minutes without a cursor on my X2 project, driving me totally mad, until I unplugged the midi cable coming out of that old converter box into my midi interface (I have an emu 0404).  The cursor magically reappeared.  Don't know if this will help anyone, but there could be something to do with weirdness in your midi setup that could cause sonar to freak out in some way.