The original clip will not mute. Anyone else having this trouble? Thanks!

Is this on existing V-Vocal clips or new ones?
 
Can't say I've noticed a problem with them muting.

One reason I switched to Melodyne was that V-Vocal clips would mute and unmute unpredictably.
 
I also think Melodyne sounds better.  It would probably be the best $100 you ever spent if you do a lot of vocals.  In addition to fixing pitch and pitch drift, I use it to correct timing, reduce breath and other non-musical sounds, and to smooth out note volumes so less compression is required.
 
I sometimes fix little artifacts like pops, but I usually find it easier to do that in the actual wave before transferring to Melodyne.  (Tip: Drag-copy your wave to another track before you start chopping it up. )
 
 
By the way, to all the haters who don't like vocal editing, I will say again that 1-Melodyne and V-Vocal are just effects like compression, EQ, etc.; 2-singers have been comping together takes for decades; and 3-when the feel is right I don't want to lose it or wear out the singer over little things that I can fix.
 
Not too long ago a musician was giving me a hard time about what he called micro-editing vocals and said, "[group name withheld] didn't need that to record [song name withheld]."  The song in question was a Woodstock-era record and I really like it and the group; but when I listen to it now, the off-key harmonies really jump out at me.  Times change.

It's on new V-Vocal clips and only in X2. I go back and use an existing project in X1 and it works fine. I've actually never had that problem before.
 
Konrad, I've been thinking about trying it. That's ALL I do are vocals. I'm a vocal producer. Yes, indeed, times change. If you want to sound like what's on the radio, performances need to be at a level of perfection most humans cannot reach. My job as a producer is to determine if the genre I'm producing calls for that non-human perfection or not. Thank goodness there is so much variety in music production these days that we as producers can make that call. :) Thanks for your thoughts!
 
Still hoping to get an answer to the problem. I'd love to solve it with V-Vocal rather than purchase Melodyne. I know V-Vocal like the back of my hand and would hate to have to slow down my workflow for a learning curve. 

I'm sure it's not worth saying this, as you seem to be a fairly experienced V-Vocaller, but make sure you work in short, clean clips with good signal level, free of bleed and with no other Fx applied.

 I indeed have experienced the same troubles. I then go to the layers and switch off the original clip. Not that I am loving it, but at least it works ;-)

go with melodyne editor2, they have a lot of good videos to help with the learning curve...

Is this only on a single project that you have this problem or is it something that recurs?
If you have a recipe for this please log a bug with a sample attached project so that we can take a look at it. I don't believe that we have any logged issue where the original clip is left unmuted. There was no change of any significance between X1 and X2 as far as this goes.
 
In the project that has this issue, there is a simple workaround: Select and cut the affected vvocal clip and paste it to a new track. You should then see the original audio clip. Simply delete it or manually mute it, and then move the backed up vvocal clip to that track. It should be fine from that point onwards. 

Staying with V-Vocal is cool if it's working for you; however, I found Melodyne super easy and the free videos on their site are great—plus I am happy to provide tips are as the other users here.  I just have the monophonic version: Melodyne Assistant.  I will probably upgrade at some point but I don't need the polyphonic version now and I don't want to take a chance on a new install corrupting my works-in-progress.