I think ichnilatis is talking about opening books from Pocketbook's library and hius07 about opening books with a specific engine within the program.
The later is something under our control. The former is not and some new FW can screw things up. Anyways the menu to setup file associations is in Settings->Device. Try to disable association for all of them and then reenable the formats you want to open in KO. That way it will override the config using the new strings used by the FW.
Again, there're chances of a new FW screwing things up or even render the "feature" unusable. YMMV.
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