has the boot been stretched at all?
how were they stored, loosely done up, tightly done up, buckles open?
did you tighten the buckles more then normal?
did you have them unbuckled skiing at all?
all of these things can affect the boot and how much water gets in, if the boot has been stretched it may have collapsed the top of the shell slightly which could cause the problem, or if the boot was stored very tightly buckled it could have distorted slightly at that area.
if they have been stretched then go to your shop and have them heat the overlap slightly, reverse it and let it cool, to get a good seal at the factory they reverse the overlaps on the boot shells when they come off the mould and let them cool this way, this helps with the continuity of the shell shape at the instep, so it can be done manually if required
some snow crystals are just very fine and will find their way into the boot
as for the black dust it looks like the plastic section at the top of the liner is rubbing on something , possibly one of the bolts in the spine of the boot, have a look round it for wear, it shouldn't be a problem
not sure an intuition liner will solve the problem, but if your foot is high volume for the boot and forcing the overlap apart a little then it might be thinner and help a little