I have Auto-Tune EFX 3 which gets the job done but inputs occasional glitches on my tracks.

They generally sound like pops and sometimes, are a bit more nastier.

Today, while mixing a song, I realized I wasn't hearing any glitches. I've had to deal with it on every other project but this one, so I find it a bit strange.

I demoed Auto-Tune 8 and I didn't have to deal with this issue, so I'm not sure why it's happening with EFX 3.

Has anyone experienced this and found a resolution or at least understand what the cause might be?

yooo! i thought i was the only one. I'm Emailing them now and have been talking to them about the issue for the past week. 
When Ever i apply Auto-Tune EFX 3 i get: pops and clicks or distortions in random spots and if i replay my track it will not be there but if i bounce it out it will be on my Bounced File, My Clients are pissed sooo. >:(  im pissed as hell, im using Autotune EFX 3 that i paied for on protools 12, and some ppl i know have no issues with the cracked EFX2 on earlier protools. 
 
Contacted Antares and im waiting to see what they say, so far they say im the only one with this issue.... i just sent them the link to your post to show that it's others with this Bug on the efx 3