If you change the time and date on the system, it will effect all messages. If you beleive that a "midnite reset" is creating the problem, you can do a quick test.
Leave a message in a mailbox, (let the system turn the MWI on) then press the F3 key and hit enter twice. this will force a system clean up.
(this is the same as a midnite reset) watch the bottom of the screen for the mailbox information. see if the mailbox in question deletes any messages. You may have to repeat this test several times.
I am not aware of any DOS issues (4,5 or 6) that effected the system operation.
However there were several problems with software versions. (From messages not deleting to DTMF problems)
I would not recommend coping file from the "zip directory" unless you have lots of experience.
If the wheels are falling off, Then reload the system disks the came with the VMS.
Note:
Power caused the biggest problems for the VMS!
If you don't have a good UPS/Conditioner for your VMS, Then go out and get a good one.
I highly recommend ONEAC.