Hello, I hope the following is of assistance.
From your description I suspect that the van is the 2 battery model and 1 of the batteries is flat. The Transit has a split charge system for charging both batteries, one battery is mainly for the starting system, the other does the electrical systems, when 1 battery goes flat you get many electrical concerns but once the van is running the charging system provides power to all systems so the inoperative systems start to work OK.
The fact the audio unit loses it's code suggests no power to it at ignition off.
When checking the batteries make sure they are disconnected from each other and the vehicle to prevent incorrect readings.
Start with the above, let me know if I can assist further or if you have more questions regarding this and I'll reply as soon as I'm able to.