Kalle Rantaaho
Double your MIDI-preparation buffer "MIDI buffers ... Prepare using xx ms buffers"
That's most common reason for randomly skipped MIDI-notes starting from SONAR 8.
I must have written this answer a hundred times during the past year.
+1 - that'll almost certainly fix it.
synkrotron
Mine is set to 250ms, which must be the default because I haven't touched it.
It is the default, bizarrely though I believe 500msecs is recommended.