actually that is specifically because of the warp fx feature of NanoFX, if you disable that, SP should work with it to some extent, although, KM wasn't designed to work in SP at all, you will most likely have problems once you switch to the Sovereign later in the game, as that ship has been designed to work significantly different to the stock one. Also, you might have noticed that although you got SP working, few of any of the mods from KM actually work in SP. your best bet to play SP with all the latest ships, is to install BCSupermod 3, although as Jimmy already said, you can't install it with anything else.