The first possibility is that the MIDI buffers are set too low in Sonar preferences. The default is 250milliseconds, but that often causes problems with MIDI playback getting scrambled. It's worth checking and if it's lower than 500ms try setting it to 500. Sometimes going even higher can be beneficial.
This buffer is not one I have messed with uey, meaning I was unaware of it. I shale have a look.
Another possibility is you are on the verge of an audio dropout. Dropouts can happen on even a lightly loaded PC because they're not always caused by high cpu or disc usage. Try increasing the ASIO buffer (assuming you have an interface that uses ASIO drivers) and see if that helps. If it does but the lag between playing and hearing the note played is a problem, then it may be time to do some troubleshooting to see if it can be lowered.
I am finding that I must make a balance between a lovely satisfied ASIO buffer and something else in there that slips my mind. The 2 seem to work in tandem,
Can Sonar play back audio tracks without problems? Does disabling effects make things better or worse?
Yes, I will give a qualified yes on that becaise I am such a perfectionist. Things are being played back.