I don't think mixing of different fuel grades or fuel from different sources should be an issue: refineries routinely blend to produce jet fuel in the first place and transfers of different grades between storage tanks are common place.
I'm not convinced by arguments based on fuel freezing - if the TAT was -37 and the fuel freeze point -57 how did it freeze? The freeze point is the appearance of crystals, not the point at which the fuel goes solid, and the margin was 20°C, not the 3°C required.
Stratification of products in storage tanks (caused by density differences) is well known in the liquid gas industry. However, stratification does not occur in ships, and this is attributed to motion. Note the design of the ships minimises sloshing at the liquid surface, it is the induced motion in the bulk fluid that prevents stratification occurring. I would suggest the continuous motion of an aircraft in flight would have a similar effect.
The odd bit in all this is that whatever happened affected both engines at virtually the same time, though the systems are supposedly completely independent. Is there some kind of (hidden) master- slave relationship between the engines buried in the software?
If I understand correctly, there are two pumps per tank - even with a master slave relationship between the engines this seems to rule out obstruction of the pump inlet screens by a foreign object or pump failure.
I think if the investigators knew the answer it would have leaked by now - which makes the whole affair ever more curious.