Have you upgraded to the most current Service Pack?
This is a noted problem: https://support.avaya.com/ext/index?page=content&id=SOLN258490&group=UG_INTERNAL

Sounds like you are affected by Case 1:

CASE 1: VM Pro - Group Mailbox Issue through SCN using Visual Voice

Using Voicemail PRO Visual Voice, intermittently getting some of the following issues:

new messages not shown in Visual Voice.
cannot access or play message showing in Visual Voice
old messages not shown in Visual Voice
already played messages shows as not read
messages showing in the list of messages do not play
messages that show in the list of messages, cannot be deleted
MWI not matching message list

Issue reported in 8.1, 9.0 SP7