Some notes being ignored

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

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.