I was having a similiar problem on my 2003 X5 4.4 with a random Trans Program Failure message. It has cleared itself, but I was getting ready to replace the neutral safety detent switch on the automatic transmission. The switch is located on the driver side of the transmission, has a mechanical shaft that actuates, and would be submerged if you went through some very high water. I had "zeroed in" on that switch as the my likely cause of my Trans Program Failure erratic messages, based on other info also on the forum. My Trans Program Failure Error has since cleared up, maybe just from working the switch quite a bit, but that is the place I would look and is something worth checking. I had also been down the low voltage path to no avail. Its more likely now the switch causing that issue on my car if it reappears. BTW, the switch is not cheap. Over $200. Electrical gremlin, or Bavarian equivelent, at work again.