This is a strange one. I'm using R-Mix on a full song audio track to filter out everything I can apart from a vocal so that I can learn the melody. I'm using a True Piano on an Instrument track to play along and record the midi and then editing in the PRV to correct it. The first problem was R-Mix adds a chunk of latency but I used the PDC button to get over that, but playing back the recorded midi I found it dropped various notes.
If I bypass the R-Mix all of the midi notes play! What kind of strange voodoo is this?
 
Grum.

Doesn't matter. I got rid of the R-Mix and just slowed down (stretched) the track, recorded a bunch of midi and then Sonar said there was a problem and crashed. Everything gone.
I can guarantee I could have done what I was attempting to do in Reason and it wouldn't crash. One audio track, one virtual instrument and a bit of midi editing and Sonar crashes.

MIDI dropping notes usually means your MIDI Playback buffer is too small.  Try a larger value on the MIDI->Playback and Recording option panel.  I don't think it has anything to do with your crash though.  R-Mix is kind of buggy though, it really needed more development instead of being dropped entirely.
 

Any plugin that induces a lot of PDC (the new LP EQ and Multiband Compressor are common offenders) may necessitate increasing the MIDI Prepare Using Buffer, especially if it's at the default of 250ms; this is too low for a lot of projects even without added PDC. The old default of 500ms is a better starting point.
 
That said, soft synth tracks should preferably be frozen/bounced to audio by the time you're using mastering plugins like these.

I appreciate the replies, and I thought the midi buffer could be involved, but I'd given up with the R-Mix anyway as slowing the audio is a better method of sussing out the pitch and timing.

I don't understand how editing midi can kill the host program. The notes I had selected started twitching (shrinking and growing by small amounts) as the mouse moved, the smart tool stuck in delete mode and then the dreaded crash window popped up.
I was seconds away from "saving as" and shutting down.

Definitely not normal. Hard to say what was going on, but kind of sounds like runaway input from a stuck keyboard/mouse button or maybe a MIDI feedback loop. Are your keyboard/mouse wireless?

Both wireless but never problematic (before). It was very weird and once it went funny a crash was inevitable I suppose.
Anyhoo, my anger has gone and I'll try again tomorrow.
This time I'll give the track a name at the start rather than the end so I can save with my normal regularity .