Overdubs Out of Sync (Solved)

Does this still occur if you bypass plugins ("E") prior to recording the background vocals? Some plugins have look ahead features that can cause issues.
 
Another item you may want to look at is PDC, but I have never really used this as I typically will bypass plugins to track in a project with anything CPU-intensive already present. The next step I would try is freezing VSTis if you have many in the project.

Sometimes adding or adjusting an effect that doesn't report it's latency correctly can cause this.
 
Sometimes an effect that does this will have different latency with different settings or prests... so it may be synced sometimes and not other times.
 
Sometimes when an effect is inserted into a project when that project is set at some particular sample buffer setting things go whacky if you change SONARs sample buffer setting. I had that happen with synthogy a couple days ago. I had changed to 1024 to work with Melodyne as a clip effect and my Synthogy instance started playing it's left and right image out of sync by a few ms. I set the audio back to a 64 sample buffer and Synthogy started acting as it had when I had recorded the part.
 
 
 
Another thing I would check, because I use a ASIO driver is the manual ASIO latency compensation setting. I have to add a manual adjustment to get perfect round trip or over dub sync. If I change my sample buffer size I also need to change the manual offset becasue it's different with each sample buffer setting.
 
Good luck!

Disabling all plugins didn't make any difference. And PDC? WTF? Thanks for the idea, Michael, but I couldn't figure that out.
There are just three synth tracks, and I didn't get around to freezing them because I first tried turning off the metronome count-in...
 

brundlefly
Out by a full measure sounds like an issue with Metronome count-in. I don't know if where you're overdubbing will allow you to disable the "gnome" and just sync to playback of existing tracks, but you might try it to see if that's the root cause.
 
EDIT - Here's an earlier post/thread about this issue: http://forum.cakewalk.com/FindPost/2392701

...and that seemed to do the trick. I didn't have the metronome playing during record - just the count-in, so I turned that off. I can't imagine why that makes a difference, but my test vocal overdub played back in sync, so thank you Dave! I'm going to finish these vocals now and if it all stays together I'll mark my question "solved." I've never had this happen before, so maybe it's technically not a bug, but it sure bugged me.

This is in X3 Producer.

It's a really weird bug because it shows up extremely rarely (for me, about 2-3 times a year). I've alerted the Bakers to this as have others, but so far, I don't think anyone has been able to provide a repeatable recipe.
 
If an earlier version of your project does this every time, consider sending it to the Bakers for analysis.