clock and ntp config lives under /mm/mynode (in the CLI) which is analogous to the "Mobility Master -> YourMM1 / YourMM2" level of config.
Items that are configured in "/mm/mynode" are not synced via DB sync.
If you configure NTP in the webUI for YourMM1 you are in effect configuring "/mm/mynode" on YourMM1. You must log into the webUI of YourMM2 and perform the same config (e.g. Config -> System -> General -> Clock) in order to have it apply.
If you really want to short cut the NTP config process, you can do it from the CLI, e.g.
ssh to YourMM1
conf t
cd /mm
ntp server 1.2.3.4
write mem
This will sync over to YourMM2, there is no equivalent webUI operation.
In the below, 5.6.7.8 and 10.11.12.13 were configured from the webUI, 1.2.3.4 was put in at /mm - you will also see it if you repeat the "show configuration effective detail" on YourMM2
(sg-vmm-p) [mynode] (config) #
(sg-vmm-p) [mynode] (config) #cd /mm
(sg-vmm-p) [mm] (config) #ntp server 1.2.3.4
(sg-vmm-p) ^[mm] (config) #write m
Saving Configuration...
Configuration Saved.
(sg-vmm-p) [mm] (config) #show configuration effective detail | include "ntp server"
ntp server 1.2.3.4 # local [/mm]
(sg-vmm-p) [mm] (config) #cd mynode
(sg-vmm-p) [mynode] (config) #show configuration effective detail | include "ntp server"
ntp server 5.6.7.8 # local [/mm/mynode]
ntp server 10.11.12.13 # local [/mm/mynode]
ntp server 1.2.3.4 # inherited from [/mm]
(sg-vmm-p) [mynode] (config) #
hope that helps
-jeff