You don't note specific times, so this may be off-base - but Is it possible that the messages are marked 'low priority' and one of the mail servers are honoring the priority setting?
See Server Configuration doc -> Router/SMTP -> Advanced -> Controls -> Advanced Transfer Controls. Do the two server have the same 'Ignore message priority' setting? (If set to 'enabled' then this is not the issue)
The Server Configuration doc -> Router/SMTP -> Restrictions and Controls -> Transfer Controls tab contains the 'Low Priority mail routing time range' that is used when 'Ignore message priority' is set to 'disabled'.
Just a thought. This has caught me a couple times over the years....