What version of CUCM and what VMWare product are you using?
I've seen some inconsistencies in syncing with NTP when using VMWare in my lab. I've had one VM build sync with 28XX series router upon build without issue and another fail. However, I had almost no issues syncing to a domain controller (AD)...just tested for the sake of ruling out issues.
These are the paths to get to each CCX logs through CLI. They may be helpful if you are having issues accessing RTMT or downloading logs through it.
If you want to download them you have to prefix "file get " and you can add one of the options (re...