Find and check the sensor value which the message center is receiving. If you can determine that the proper signal value is being sent to the MC, then the problem is in the MC itself.
Most electronic devices in vehicles will develop bad internal components with age.
I've learned about that concerning several items in all 1985-1992 Mark VII's. The radios, message center, EATC, and overhead console(compass), they all develop bad capacitors, and can be rebuilt. There is a well know member of the Mark VII forum who rebuilds those devices.
I would bet that many Explorer owners are beginning to experience problems with the same items in their trucks.
That symptom of having the message center beep at you each time you turn on the key, I've had that happen in my LSC every time for about three years. I just found out about the answer last year, the guy I mentioned charges about $100 for each of those mentioned items. I expect that there are lots of places which can rebuild the message center.
With age they all will likely develop the same problems. I have an AC issue in my 98 that may well be the EATC unit. Regards,