The first one, not to insult you, is to check that your L/R markers aren’t in the wrong place…
Could be a rogue plugin, many people suffer from this. You could selectively remove 1/2 the plugins and 1/2 again etc. until it works. Then render the plugin’s effect.
Odd that it would work for MP3. You could also try some other export settings like bitrate, bitsize, see if that’s causing it.
Perhaps there’s a tricky section in the middle? I’ve had projects which are fine except for example when 20 BV tracks come in, and at that point there’s a big glitch.
I also tend to avoid running Autotune live as an insert for final mixing, seems more reliable to render it using offline processing.