If this is reproducible even with a simple project it might be useful to record a video of the steps you are taking to do this. Its not clear from what you say exactly what the sequence of operations is. Which tool is selected, is it a simple ins track, does the track contain data, etc etc.
Its not causing any problems here as far as I can see. 

Ok.
 
The pencil tool is for clicking down notes. one here, one there.
If I click and drag as if to lasso select notes, the pencil tool faithfully lays down a small stream of notes before it chokes on it and freezes up. Makes a buzzing sound as the tightly packed notes sound off, then dies.
 
I'll try tonight with a small project or even blank file and report back.
 

Could be buffer size related? (my thinking is Sonar tries to keep up but can't.)
PinkCigar described the symptoms unprompted so it's clearly real and reproducible on two machines.
If it goes back to X1 (verifiable?) then it's unrelated to recent optimizations.

bitman
If I click and drag as if to lasso select notes, the pencil tool faithfully lays down a small stream of notes before it chokes on it and freezes up. Makes a buzzing sound as the tightly packed notes sound off, then dies.

 
I can't reproduce. If I click and drag, the note just gets longer.

Ok well my results so far are inconclusive.
On a hunch I changed which device was the master clock and which device was the slave. (I have a lightpipe connection) with regards to my pre and it's receiver card because I also have other weird here and there problems.
 
Now doing what crashed Sonar now sprays notes as expected.
That said I don't know if what I'm seeing is only after some editing with other tools or if it's fixed. Time will tell.
 
This did not fix my solo playback issue which is detailed in another thread, sadly, I thought it might.

Anderton

bitman
If I click and drag as if to lasso select notes, the pencil tool faithfully lays down a small stream of notes before it chokes on it and freezes up. Makes a buzzing sound as the tightly packed notes sound off, then dies.

 
I can't reproduce. If I click and drag, the note just gets longer.

I get the quarter notes as I drag. No crash.
 
How do you get it to drag as long as you want?
 
 

bitman
On a hunch I changed which device was the master clock and which device was the slave. (I have a lightpipe connection) with regards to my pre and it's receiver card because I also have other weird here and there problems.

FWIW, I often have my MOTU interface slaved to ADAT from an Alesis QSR because the Alesis doesn't like to be a slave. I have no trouble drawing notes as described with a track outputting to TTS-1 or SD3 either way.

There is a curious thing happening here. As I posted earlier I still have no crash but not what I think should happen.
What I am experiencing only happens with Session Drummer.
Here are the steps that so far are very reproducible.
New project no name (not likely relevant)
Insert synth from synth rack (simple instrument) so far must be Session Drummer.
Load program in SD and drag a clip to the first measure.
Leave synth properties for SD open and double click the clip you drug over launching PRV (docked).
Select the pencil tool (smart tool will not reproduce).
Drag diagonally in PRV to right of notes from clip. (multiple notes are produced, this is not the case if you use smart tool).
SD synth properties begins looping a clip from the loaded program. (if you watch the SD properties window it is getting buttons selected and seems to be responding to the mouse as you drag. This is on my laptop so the location of the SD properties window is restricted with regard to the PRV).
SD will start looping a clip from the program. If you clik the stop button in the SD properties it will stop.
No crash for me just a loop fest.

notscruffy2
 
SD will start looping a clip from the program. If you clik the stop button in the SD properties it will stop.
No crash for me just a loop fest.

Following your instructions I did not get any looping. As I put the notes in they sounded as expected. But no looping.

Session Drummer starts playing the loops if you trigger some low MIDI notes.  When I drag the MIDI clip into the trackview it seems to include a kind of "drum map",  at the bottom of the PRV are listed notes 0 - A, 1 -B, 2 -C, etc that if you draw on with the pencil they start playing that loop in Session Drummer.  Not really sure how it gets named MIDI notes like that, it's not a drum map.  Some sort of instrument feature I never use I guess.