I think you have to find out which component the PMS is sending check-in/checked-out commands to (usually a hotel voicemail system).
When PMS sends check-in(s), the VM system buffers the request(s) and does the following:
1) Opens the extension for outbound dialing (a COR) setting.
2) Opens the VM Box,
3) Opens maid codes, bar, etc usually called hospitality features.
So, I'd do this: Check the set programming of a room not checked in compared to a room checked in (you should see a COR difference between the two) but the key item is the FRL. You may be able to make the COR change in the Voicemail systems logic...
If not - The checked-in room will have a higher FRL (0 to 7) than the checked-out room.
Then, change the COR of the checked out room to match the FRL of the checked in room.