I'm using Kontakt's Scarbee Bass in Band In A Box and there are missing low notes during playback.
I've tried several different settings in Kontakt but nothing fixes the issue.
Any ideas?

When you view the virtual keyboard in the Kontakt GIU are notes being played below the playable range of the instrument?  If so you may need to transpose the part up an octave.

Yes.
However, when you transpose the instrument up an octave, it sounds an octave higher but the lower notes are still appearing in the red section.
Frustrating.
 

Band in a Box must be generating notes outside the range of a bass guitar. Scarbee basses do have retuned samples down to B extending the range by 5 semitones, if you want to go lower I suggest a synth bass.

The bass track stays in range, like Ab2, but Scarbee just doesn't want to cooperate.

If the notes are appearing in the red section of the Kontakt virtual keyboard (the keyswitch region) they are out of the instruments range. There are no samples on those key so no way will you get a sound.

Question is why, maybe some band in a box users will comment if you change the title so they notice it, but it has to be a transposition issue.

If the notes are in range, ie in the playable range of the virtual keyboard) and still won't sound, check the velocity and any other cc data. Remember the Scarbee basses have velocity switching for different articulations. (which Scarbee bass by the way?)

Yes it is a transposition issue.  In BiaB click on preferences/channels and raise the bass one octave, especially if you are going to use that bass as your go to bass.  Otherwise raise the bass's octave in Sonar.  In this scenario those are your only two options.

I have now got to my DAW and have been investigating further.
  
The Scarbee MM bass manual gives the range of the instrument from B0 to E4. When I enter notes in Sonar in this range it works as expected. Note numbers are confirmed in the event list.
  
Velocities below 40 play as mutes and 40 and above as sustains. Even at a velocity of 40 the sustain is clearly audible so I doubt if that is causing the problem of non sounding notes, it may however cause things to sound a little different if the MIDI is expecting a smooth velocity curve from 1-127. You may get quiet notes sounding as full volume mutes for example. I think the other Scarbee basses use a similar system but there may be some variations, for example Pre-Bass will sound harmonics for velocities <15.
 
I don’t think the legato triggered hammer on articulations are relevant to you problem but it’s worth understanding how this works as it may cause bass parts not written specifically for the instrument to sound odd in places.
 
If you are using Sonar, check the setting for "Base Octave for pitches" in preferences, customisation, display. In my setup this is set to -2 (the default) and with this setting Sonar and Kontakt are using the same convention. If Band in a Box has a similar setting and its set to something different this may be why you think your notes are in range when they are not.
  
I can't think of anything else I can try without Band in a Box.
 
edit - MarioD beat me to the Base octave thing while I was typing.

I can tell you from experience using Scarbee Jay-Bass if some notes are held longer than the notation shows it will choke off the attack of the next note! Example-You record a performance of a bass track and you are playing just quarter notes. When you check the note editor for the duration the note was held down, the duration could be just a click or two too long. Quarter note equals 1:000, but the duration you held the note down was 1:006! If you edit that note back to 1:000 the attack magically reappears. I don't know how you would edit those notes in BIAB but that will fix problems with the pluck not being heard.

Sidroe
I can tell you from experience using Scarbee Jay-Bass if some notes are held longer than the notation shows it will choke off the attack of the next note! Example-You record a performance of a bass track and you are playing just quarter notes. When you check the note editor for the duration the note was held down, the duration could be just a click or two too long. Quarter note equals 1:000, but the duration you held the note down was 1:006! If you edit that note back to 1:000 the attack magically reappears. I don't know how you would edit those notes in BIAB but that will fix problems with the pluck not being heard.

I assume you mean the hammer on and pull off articulations that are triggered in place of the normal sustain articulation when notes are played legato with a slight overlap. There is somewhere on the web a video of Thomas Scarbee demomstrating the features and explaining how he wanted to make a instrument he could play live that replicated the control he had playing a real bass because he was suffering from arthritus and was no longer able to play bass well. I will see if I can find it.
 
Edit - Here it is https://www.youtube.com/watch?v=2ZBFnR7IckQ It was carple tunnel he was suffering from. However the discription of the hammer-on and pull-off must be elsewhere.
 
Edit again - here https://www.youtube.com/watch?v=SS4FdAua0_o