NKS only contains the full bank of a plugin, not individual presets. As such, some plugins are incompatible with the way NKS is implemented (or rather: NKS is incompatible with these plugins). Until Native Instruments decides to fix NKS, there's nothing much PresetMagician can do for you there.
To test if the plugin in question is compatible with NKS:
Open the plugin in Maschine or Komplete Kontrol
Pick a random preset from within the plugin
Save the NKS file using Maschine or Komplete Kontrol
Pick another random preset
Load the previously saved NKS file
If the preset doesn't change, it means that it isn't compatible with NKS
Some plugins also have bugs, where they give back their bank data but unable to load them again.