This is a strange one. I have a MIDI bass pattern that's playing a C6 instead of the C5 as written. If I click on the note to hear it, the correct C5 is played. But upon playback Sonar is playing a C6. I've tried deleting the note and drawing it in again - same thing. There are plenty of other C5's in the same clip and they all play correctly. Doesn't matter what velocity I set either. There is no other controller data going on. 
 
For what it's worth, the bass instrument is Trilian. 
 
Any ideas? To tell you the truth it sounds kind of cool to have that high note pop out, but things like this worry me when I'm working on a project. 

UPDATE: There another strange thing going on in the same clip. I have a three note phrase a little later in the clip that is C5, C4, C5. If I start playback exactly on the first note of the phrase, all three notes are played as C5. If I start playback a little earlier, the correct notes are played. What is going on?

Does the setting of Edit > Preferences > Customization > Display "Base Octave for Patches" come into play here or does Trillian have a similar adjustment.
 
Your other issue sounds like the synth needs a little time before processing notes.

It's not the "Base octave for pitches" option because other notes are sounding correctly. Trillian has a base octave control too and adjusting that makes no difference, i.e. if I raise it an octave then the same problem occurs only an octave higher. 
 
I've tried various values for the MIDI buffer and also tried whacking my audio buffer up in various increments, but no joy. 
 
In fact trying playback from different positions in the clip creates different kind of note errors. For instance, starting from one particular note results in Sonar playing the note previous to it first (and then it screws up the octave of the note after the next note). 
 
Hmm, Sonar appears to have a problem with Trilian in a way I've never encountered before. I've tried outputting the clip in question to other instruments and it plays fine. 

Some extra information in case it's relevant: The bass part in question was generated from playing another bass part through the arpeggiator and then bouncing it to a MIDI clip. I wonder if doing that bounce has corrupted the MIDI data somehow? 
 

Have you looked at the MIDI data in the event list?

scook
Have you looked at the MIDI data in the event list?

Yep, nothing out of the ordinary there. Everything is as it should be. 

Try it with a different synth & see what happens.
 
Load up a bass patch in Dim Pro, copy the Midi from your Trillian track to the DP Midi track.

Jones I think he said he did that and it played fine.

my suggestion would be copy the clip to another instance of Trillian and see.what happens. If it still does it, I'd look at Trillian.

I'm thinking that it may be Trillian by now.
 
Long shot, but is it a S.I.T. or a synth track + MIDI track?  If the former, is it worth splitting it?  It can't hurt to try.
 
I'm sure I've had a similar issue to this before, but can't for the life of me remember the outcome.