Centaurus - Sadly I have no documentary evidence to support my reference to Boeing's feedback. At the time discussions were definitely held between the Fleet Manager's Office and the manufacturer, but this was only summarised by way of a Notice to Crew, or similar.
Ironically, I was (unsuccessfully) seeking a copy of that very notice some years later as the same company had a different policy on their 737 fleet! (Anecdotally, I understand the 737 has had similar false config warnings - also due to corruption of circuit boards buried somewhere in the E&E compartment.)
As an aside, I wonder about the possibility/likelihood of a slat retracting during the takeoff roll. Even if it is possible, I would have thought a "slat-generated" warning would be much more likely to be caused by a problem with a micro-switch/proximity sensor instead of something that should be hydraulically locked in place.
In the end, it all gets down to "balance of risk", which is invariably assessed with the wisdom of hindsight!