A couple of thoughts:
Like many bass synths, SI Bass is transposed up an octave so you can more easily perform bass parts on a 61-key keyboard without transposing the keyboard. This means that parts played in a normal range (e.g. 3rd-party MIDI clips intended for GM synths) may go below the range that SI Bass can play, resulting in missing notes. Try transposing the track up 12 half-steps using the Key+ (Key Offset) setting in the Inspector for the MIDI track (or MIDI tab of an Instrument track).
In trying to replicate a problem I found that many patches SI Bass patches (especially muted patches like 'Picked Mutes') have a really odd/variable attack that can make the timing of some patterns sound really wonky. Try the 'NiceBass' patch as reference; this one sounded fine to me with once the part was transposed up.
Both of the above issues are somewhat more obvious when the track is soloed.