I played a simple drum track with Superior Drummer and I noticed that most of the data was being ignored. Then I noticed the same thing happening with a one-note Trilian bass line. Here's the curious thing:
 
When they played a note, they played at the same time!
 
That surely means it can't be an issue with either vendor's product? Something else must be going on but I can't think of anything that would make two different vendor's plugs play at the same point in time - ONLY - and ignore the rest of the notes.
 
Has anyone seen that one before?
 
Thanks - rev

I found the problem it was the Kjearhus MPL-1 Pro compressor I had in the Master bus.
 
As long as that plug was in the signal chain, other plugs misbehaved, maybe the MPL-1 is in Demo mode.

The most common cause of dropped MIDI notes is too small a MIDI 'Prepare Using' Buffer in preferences. Try raising it to 500ms or higher as necessary. A lot of projects have trouble with the 250ms default, especially if they include PDC-inducing plugins.

Brundle:
I thought I'd found the problem but it turns out to be happening with various instruments. I'll try your buffer suggestion and post back.
You're a genius! That seems to have fixed it. I was at my wits end, not knowing who's dropping the ball, was it Kontakt, the plug, Sonar itself. 
Thanks a million for that!
Now I have a delay when notes are clicked in the Staff View. The notes play on time in Playback so it's not a big deal but it's another quirk that wasn't there before I had to reinstall everything. 
 
rev

The latency when clicking to play notes likely has the same root cause as the dropped MIDI notes: You have some FX in the project that uses a lookahead buffer that induces added latency and requires everything to be delayed by the same amount to play in sync (Plugin Delay Compensation). Common offenders are convolution reverbs, and Cakewalk's own Transient Shaper and Linear Phase EQ and Compressor plugins. Disabling all FX temporarily by hitting the 'E' shortcut or FX button in the mix module will tell you if this is the cause. It's best to avoid using such plugins until you're past the tracking/composing phase of the project, and on to Mixing/Mastering. But PDC can be bypassed for recording live inputs by clicking the PDC (bypass) button in the Mix module.

Got it. It's fine in playback, the delay only happens when entering notes with the mouse. Now that I know it's the 'new normal' I'm not concerned about it. 
Thanks!