456gt window and central locking issue

Before checking problems with the ecu, I would try checking inside the door handle lock mechanism. If you can remove the door panel, try testing by manually moving the 2 rods that connect the interior door handle and lock to the motor.

Pulling the interior door handle is also what activates the motor to lower the window. On older cars the metal moving parts can become very dirty and sticky, not allowing the door handle and locks to move freely. This can cause all kinds of issues related to what you're experiencing

 

You shouldn't need to adjust the actual rods, the main issue are the rotating levers they're attached to which push/pull the rods. Those metal on metal parts may need to be cleaned and re-lubricated to unstick them.

Here's a picture of the parts I'm talking about:

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My 2001 also has sticky door locks. Pushing and pulling on the rods feels like the lubricants in the door locking mechanism has aged and getting gunky. How difficult was it to get in there to clean and re-lube the locking mechanism?

 

Since the door closes and opens (using the interior/exterior handles) and locks (mechanically) with the key, personally, I would think it would be an electrical switch issue or even a Window ECU issue. Unfortunately, there are 8 or more door and window position-sensing switches on the 456.

According to past posts on FerrariChat, there are at least 3 switches which control the window drop/close function when the door is opened/closed. The inside door handle switch and the outside door handle switch (for window dropping) and the switch on the hook on the door pillar (for window closing). However, you would think that at least one of these would work. Of course, there may be one switch overriding the others (e.g. perhaps the door pillar hook switch telling the system that the door is closed, so the "door open" switches are not dropping the windows?)

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Try giving the hook switch a spray with electrical cleaner. You may be able to remove the hook and check the operation of the switch with an ohmmeter.

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If the switch is intermittent, try swapping the passenger and driver's hooks to see of the window problem transfers (They have the same part number: 63157000)

However, if this switch also tells the Window ECU that the doors are closed, allowing the central locking system to lock the doors, this kills my theory. A permanent "door closed" signal will not stop the doors locking with the fob.

Unfortunately, there are no useful wiring diagrams for the door/window electronics (so there is no way of checking switch function at the ECU) and the names of the switches in the Workshop Manual are very confusing.