I recently installed this program (and works great) but I was having some intermittent dropout problems when it was used.  I had been adding the Auto-Tune to what other effects were already there for the vocal tracks. I had tried increasing buffers but that didn't help.  I found out that if I add the Auto-Tune as the first "effect" in the effects list (probably where it should go anyway) the dropout problem is fixed. 
 
 
 

Yes, it's rather obvious that the program can't determine the pitch if the sound has FX harmonics, distortion or such.

I strongly recommend bouncing the Autotuned track and adding the rest of the FX to that audio track.

What Autotune, V-Vocal or Melodyne Plugin do is so complicated a task including pitch, timing, formant etc. (not to mention having maybe several such tracks in the project), that leaving it active in the project is begging for trouble, I believe.
I've had my share of problems with Melodyne Plugin. Projects refused to open, hung audio, audio could not be edited and else.

Good idea on the bouncing.  Run it first with the Auto tune and then do whatever else is needed later.

I have Auto-tune EFX 3 and I was getting a lotta clicks/pops. Especially with the vst3 version. Started using the vst2 version and it made a huge difference, but is still not perfect. I still get the popping but hardly. I don't seem to have this issue with Antares' flagship software, so I find it a little strange. I can't have this for a plugin I depend on so much when mixing vocals.  

fireberd
I recently installed this program (and works great) but I was having some intermittent dropout problems when it was used.  I had been adding the Auto-Tune to what other effects were already there for the vocal tracks. I had tried increasing buffers but that didn't help.  I found out that if I add the Auto-Tune as the first "effect" in the effects list (probably where it should go anyway) the dropout problem is fixed. 
 
 
 

Which version of EFX is this related to?
I have version 3 and the popping sound I'm getting on my tracks is killing me!

Same here using vst3 and snaps crackles and pops all over the place... I will try vst2 when I get home today. Anyone figure out anything else?

Yes, Antares recommended using the vst2 version of EFX3, as there are known issues and updates/patches to vst3 are doubtful. Same for the Harmony engine. Using the vst2 for both and placing it first improves its use, but I'm still get the odd dropout and pops...mixing down is a good way to go.