I'm on site investigating as I type this. The set showed it has a message - confirmed the button flashing was a VMMSG key, the lamp on the display was also flashing and the display showed '1 new message'. Logged in to OSDM and the mailbox showed no new and no saved messages. So I pressed his flashing voicemail key and the voicemail said "you have no new messages" - and the lamp cleared. This happens a couple times a month.
This site also has SPNET, but i've not set up any message forwarding between systems - only extensions for users to dial the far end and let the far end handle the voicemail for that system's user.
I also noticed there was programming in MMC 505 (administration not tech programming) for NTP with PST time zone settings, but in the voicemail under system parameters, the time was set for GMT. So i'm wondering now if that caused the voicemail to mis-tag the message with the wrong time envelope. I've made them the same and will see if it happens again for delayed message.
I should schedule to upgrade the software to 4.80 as well and see if that clears the voicemail indication issue.