I guess you assigned the notes to each keys, using Xkey plus software ?
When you connect your Xkey, the soft reads your entire configuration from the keyboard, when selecting the notes that fail, can you see the correct assignment ?
Can you please send screenshots that show these notes configurations in Xkey plus ? please send to [email protected]
Did you try to connect a MIDI monitor (snoize on Mac or Midiox on win) to check the notes generated by your Xkey ?
To finish, please let me know your Xkey model as well as Xkey plus version.