'Probably get it then; thanks for validation about it working in X3.  ('Saw 6 videos already)
 
So you are using Editor (vs Essential) ... hope your problem is not specific to Editor.

Not specific to Editor, AFAIK.
 
Has been working perfectly here until just now.

I'm using Editor and I went through all the Groove 3 tutorial exercises over the last few days. So far nothing reproducible but I'll keep my eye on it.

Is there a tempo change in the project?

Weird things can also happen with the positioning of your Melodyne clips if you insert measures in a project.

Thanks Jb. It's great to hear your validation! I just ordered Melodyne editor 2.0 and am watching it download here at a motel. It's very slow here.

It's great to have this program that I need ... And hopefully to be able to do a lot of surreal time, melodic, and loudness functions that the videos inspired.

Interestingly, I've never had the latest versions crash sonar. The program has actually suggested for me to change my sampling rate which helped.

Utmost blessings/regards,

Hope you enjoy it, Philip.  I have found it to be a remarkable piece of software.
 
Which makes it all the more frustrating to have this strange issue.
 
It makes using Melodyne useless to quantize notes.  I am sure I remember someone having a similar issue.
 
Any further help will be greatly appreciated.

I have the identical issue.  I'm using X3d and Melodyne Editor 2.  I have a rate of 142 bpm, don't know if a faster tempo affects it.  I'm using Melodyne to true up timing on vocals.  I mostly do it by ear, I'm not quantizing so cannot comment on how it affects that. 
 
When I need to align to the beat visually, I've been lining up the Now marker in the Track View at the top of my screen to the beat I want, then using the time marker in Melodyne as the reference to drag my note beginning or end to match.  It's visually not lining up with the same beat on the Melodyne grid, but in reality it IS aligning to the correct beat in Sonar (confirmed visually with the waveform after closing Melodyne.)  Not really much of a pain, since I keep the Track View open at the top of my screen.  I just have to remember to refrain from using the "obvious" time grid in Melodyne.
 
I upgraded to Editor 2 immediately, so I haven't used Essential and can't comment on if it was there before - but I noticed this issue immediately, so it doesn't seem to be an "I accidentally turned something off" issue.  And it's there all the time, even after re-booting.
 
It seems I remember having the same time-grid alignment issue at some point in V-Vocal too?
 
Despite this isse, I LOVE Melodyne.  Absolutely worth every penny from my perspective, I've been giddy just using it.

This issue has been confirmed and the culprit tracked down, it seems.
 
If anyone wants to know the details then feel free to PM me.

It seems to make Melodyne's Quantise Function in Sonar unusable most of the time.
 
I am surprised that so few people have yet come across it.  It is now "being investigated by our development team",     which is good.