Melodyne unable to process

In 1. above are you bouncing to a new clip?  That's what I do.  And I don't use freezing.
I keep the original track and open underneath it a 'treated' track, in case I want to revisit what I've done.  I chop the original track up into small bits as I've always had lockups then crashes with Melodyne versions after the good old (obsolete) Plugin version.  I insert Melodyne as an FX on the original track, muting any other FX if there.  Make sure the velocity is what you want as it will be bounced at that.  I work on the first clip and when done I highlight (i.e. select) that clip and then use the bounce to track function to bounce the clip to the treated track.  Until Melodyne's resource leak is fixed I then have to save the project, delete the Melodyne plugin, close and re-open Melodyne (yes, exactly...)  I then do the next clip and so on.
 
NB: Melodyne acknowledged the resource leak after CW told them about it in January following crash dumps I (and others I assume) submitted to CW via Expanded's new problem reporter.  Melodyne have promised a fix but in the next Editor V2 update.

I have the bounce-to-clip function bound to a key.  It's been the same forever and has worked until recently.  I definitely am bouncing the clip because it's visual when it does so.

I use the version of Melodyne that was right before the new 2.0 version.  They came out with the direct-note DNA thing, and I got that upgrade for free and haven't upgraded since because it's been working for me.  I don't upgrade unless I either have to or want a new feature haha

Anywho, I will try out the 'proccess effects' command I've read about.
I will also think about paying the $100 and upgrading to the latest version, although it seems a bit dumb to upgrade only to deal with a memory leak that causes everyone problems :S

Yes the time code based effects have been broken in X1D. However you can use a real time bounce to work around this. Or use 8.53. Melodyne worked great for me until X1D. Antares is not working properly either. It process just not what you want it to. This is since X1D. Cakewalk is aware and working on it.