I have two ESX environments where I have seen similar as well. How many sockets and cores do you assign to your VM’s? VMware does behave funny when you assign multiple CPU to a machine which can have a negative effect on performance. It’s something to do with waiting for ESX to free up the number of processors you assigned to the VM before allowing a VM to use it. If something changed with FreePBX 13 that requires more cpu horsepower such as cronjobs then this could be the issue. It’s better to have one 1 Ghz processor than two 500Mhz processors.
I say this like I have solved my issue, but I have not been able to figure this out either. With the new firewall module in FreePBX 13 I was hoping fail2ban could go away because when I do a freepbx reload, Fail2Ban makes my box very busy for about 10 seconds afterwards.
This problem affects all my FreePBX13 deployments on ESX, but only a few people complain about noticing it. Likely only the busier systems have users that notice the audio drop.